Genetic variation and effective population size in isolated populations of coastal cutthroat trout

Following glacial recession in southeast Alaska, waterfalls created by isostatic rebound have isolated numerous replicate populations of coastal cutthroat trout (Oncorhynchus clarkii clarkii) in short coastal streams. These replicate isolated populations offer an unusual opportunity to examine factors associated with the maintenance of genetic diversity. We used eight microsatellites to examine genetic variation within and differentiation among 12 population pairs sampled from above and below these natural migration barriers. Geological evidence indicated that the above-barrier populations have been isolated for 8,000–12,500 years. Genetic differentiation among below-barrier populations (F _ST = 0.10, 95% C.I. 0.08–0.12) was similar to a previous study of more southern populations of this species. Above-barrier populations were highly differentiated from adjacent below-barrier populations (mean pairwise F _ST = 0.28; SD 0.18) and multiple lines of evidence were consistent with asymmetric downstream gene flow that varied among streams. Each above-barrier population had reduced within-population genetic variation when compared to the adjacent below-barrier population. Within-population genetic diversity was significantly correlated with the amount of available habitat in above-barrier sites. Increased genetic differentiation of above-barrier populations with lower genetic diversity suggests that genetic drift has been the primary cause of genetic divergence. Long-term estimates of N _e based on loss of heterozygosity over the time since isolation were large (3,170; range 1,077–7,606) and established an upper limit for N _e if drift were the only evolutionary process responsible for loss of genetic diversity. However, it is likely that a combination of mutation, selection, and gene flow have also contributed to the genetic diversity of above-barrier populations. Contemporary above-barrier N _e estimates were much smaller than long-term N _e estimates, not correlated with within-population genetic diversity, and not consistent with the amount of genetic variation retained, given the approximate 10,000-year period of isolation. The populations isolated by waterfalls in this study that occur in larger stream networks have retained substantial genetic variation, which suggests that the amount of habitat in headwater streams is an important consideration for maintaining the evolutionary potential of isolated populations.     

Small effective population sizes of two remnant ocelot populations (<Emphasis Type="Italic">Leopardus pardalis albescens</Emphasis>) in the United States

Threatened populations are vulnerable to the effects of genetic drift and inbreeding, particularly when gene flow is low and the effective population size is small. Estimates of effective population size (N _e ) provide important information on the status of endangered populations that have experienced severe fragmentation and serve as indicators of genetic viability. Genetic data from microsatellite loci were used to estimate N _e for the 2 remaining populations of the endangered ocelot (Leopardus pardalis albescens) occurring in the United States. Several methods were used to calculate N _e , resulting in estimates ranging from N _e  = 8.0 (95% CI: 3.2–23.1) to 13.9 (95% CI: 7.7–25.1) for the population located at the Laguna Atascosa Wildlife Refuge in Cameron County, Texas. The ocelot population in Willacy County, Texas, had N _e estimates of 2.9 (95% CI: 1.7–5.6) and 3.1 (95% CI: 1.9–13.5), respectively. Estimates of N _e in both populations were below the critical value recommended for short-term viability.     

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction‐site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small N_e (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome‐wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high F_ST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high F_ST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small N_e in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.     

Spatial and temporal variation of genetic diversity and estimation of effective population sizes in Atlantic salmon (Salmo salar, L.) populations from Asturias (Northern Spain) using microsatellites

Rivers in Asturias (northern Spain) constitute the southern limit of the distribution of Atlantic salmon (Salmo salar L.) in Europe, a biological resource facing one of the more serious challenges for conservation today. In this work, eight microsatellite loci have been used to analyse samples collected in 1993 and 1999 from four Asturian rivers (Esva, Narcea, Sella, and Cares), obtaining information about the temporal and the spatial genetic variation in these populations and, in addition, estimations of their effective population sizes. The temporal analysis revealed a general decrease in all the estimated genetic variability parameters when samples from 1993 (mean A ₍₁₉₉₃₎ = 6.47, mean H _O(1993) = 0.472, mean H _E(1993) = 0.530) were compared with those obtained in 1999 (mean A ₍₁₉₉₉₎ = 6.16, mean H _O(1999) = 0.460, mean H _E(1999) = 0.490). This reduction was particularly notable for the case of the Esva river. Our results pointed to a pattern of spatial genetic differentiation inside the Asturian region (F _{ST (1993)} = 0.016 P < 0.01; F _{ST (1999)} = 0.023 P < 0.01). Using the standard Temporal Method we found estimates of N _e^{^} _(Esva) = 75.1 (33.2–267.2); N _e^{^} _(Cares) = 96.6 (40.0–507.5), N _e^{^} _(Sella) = 106.5 (39.1–9396.4) and N _e^{^} _(Narcea) = 113.9 (42.0–3693.3). The use of likelihood-based methods for the N _e^{^} estimations improved the results (smaller CIs) for the Esva and Cares rivers (N _e^{^} _(Esva) = 63.9 (32.3–165.3); N _e^{^} _(Cares) = 76.4 (38.8–202.0) using a Maximum likelihood approach) and suggested the presence of larger populations for the Sella and Narcea rivers (N _e^{^}≈200). These results showed that the Asturian Atlantic salmon populations (in particular Esva and Cares river populations) could be close to the conservation genetic borderline for avoiding inbreeding depression although we discuss some implications of the analysis of temporal genetic change in populations with overlapping generations.     

Influence of translocation strategy and mating system on the genetic structure of a newly established population of island ptarmigan

Island populations and populations established by reintroductions are prone to extinction, in part because they are vulnerable to deterministic and stochastic phenomena associated with geographic isolation and small population size. As population size declines, reduced genetic diversity can result in decreased fitness and reduced adaptive potential, which may hinder short- or long-term population viability. We used 32 microsatellite markers to investigate the conservation genetics of a newly established population of Evermann’s Rock Ptarmigan (Lagopus muta evermanni) at Agattu Island, in the western Aleutian Archipelago, Alaska. We found low genetic diversity (observed heterozygosity = 0.41, allelic richness = 2.2) and a small effective population size (N _e  = 28.6), but a relatively large N _e /N ratio = 0.55, which was attributed to multiple paternity in 80% of the broods and low reproductive skew among males (λ = 0.29). Moreover, successful breeding pairs were less related to each other than random male–female pairs. For conservation efforts based on reintroductions, a mating system with high rates of multiple paternity may facilitate retention of genetic diversity, thereby reducing the potential for inbreeding in small or isolated populations. Our results underscore the importance of quantifying genetic diversity and understanding the breeding behavior of translocated populations.     

A genetic demographic analysis of Lake Malawi rock‐dwelling cichlids using spatio‐temporal sampling

We estimated the effective population sizes (N_e) and tested for short‐term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro‐endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D‐loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all populations. Yet, genetic diversity was relatively low for the sequence data. Microsatellites yielded mean N_e estimates of 481 individuals (±99 SD) for M. benetos and between 597 (±106.3 SD) and 1524 (±483.9 SD) individuals for local populations of M. zebra. The microsatellite data indicated no deviations from mutation–drift equilibrium. Maylandia zebra was further found to be in migration–drift equilibrium. Temporal fluctuations in allele frequencies were limited across the sampling period for both species. Bayesian Skyline analyses suggested a recent expansion of M. zebra populations in line with lake‐level fluctuations, whereas the demographic history of M. benetos could only be estimated for the very recent past. Divergence time estimates placed the origin of M. benetos within the last 100 ka after the refilling of the lake and suggested that it split off the sympatric M. zebra population. Overall, our data indicate that micro‐endemics and populations in less favourable habitats have smaller N_e, indicating that drift may play an important role driving their divergence. Yet, despite small population sizes, high genetic variation can be maintained.     

Effects of population characteristics and structure on estimates of effective population size in a house sparrow metapopulation

Effective population size (N_e) is a key parameter to understand evolutionary processes and the viability of endangered populations as it determines the rate of genetic drift and inbreeding. Low N_e can lead to inbreeding depression and reduced population adaptability. In this study, we estimated contemporary N_e using genetic estimators (LDNE, ONeSAMP, MLNE and CoNe) as well as a demographic estimator in a natural insular house sparrow metapopulation. We investigated whether population characteristics (population size, sex ratio, immigration rate, variance in population size and population growth rate) explained variation within and among populations in the ratio of effective to census population size (N_e/N_c). In general, N_e/N_c ratios increased with immigration rates. Genetic N_e was much larger than demographic N_e, probably due to a greater effect of immigration on genetic than demographic processes in local populations. Moreover, although estimates of genetic N_e seemed to track N_c quite well, the genetic N_e‐estimates were often larger than N_c within populations. Estimates of genetic N_e for the metapopulation were however within the expected range (<N_c). Our results suggest that in fragmented populations, even low levels of gene flow may have important consequences for the interpretation of genetic estimates of N_e. Consequently, further studies are needed to understand how N_e estimated in local populations or the total metapopulation relates to actual rates of genetic drift and inbreeding.     

Drift happens: Molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus F_ST = 0.32, F_ST’ = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R² = 0.51) and higher local inbreeding (R² = 0.22). Populations varied greatly in levels of local inbreeding (F_IS = 0.2–0.9) and F_IS increased in more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.     

INCREASED PROBABILITY OF EXTINCTION DUE TO DECREASED GENETIC EFFECTIVE POPULATION SIZE: EXPERIMENTAL POPULATIONS OF CLARKIA PULCHELLA

We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (N_e), were maintained as isolated populations in a natural environment. After three generations, the low N_e treatment had significantly lower germination and survival rates than did the high N_e treatment. These lower germination and survival rates led to decreased mean fitness in the low N_e populations: estimated mean fitness in the low N_e populations was only 21% of the estimated mean fitness in the high N_e populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high N_e populations were still extant, whereas only 31% of the low N_e populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.     

Trapped within the city: integrating demography,time since isolation and population‐specific traits to assess the genetic effects of urbanization

Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments are poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; N_e) and patch size on genetic diversity, population structure and contemporary N_e. Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent N_e declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary N_e, while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provide some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted.     

Early detection of population fragmentation using linkage disequilibrium estimation of effective population size

Population subdivision due to habitat loss and modification, exploitation of wild populations and altered spatial population dynamics is of increasing concern in nature. Detecting population fragmentation is therefore crucial for conservation management. Using computer simulations, we show that a single sample estimator of N _e based on linkage disequilibrium is a highly sensitive and promising indicator of recent population fragmentation and bottlenecks, even with some continued gene flow. For example, fragmentation of a panmictic population of N _e = 1,000 into demes of N _e = 100 can be detected with high probability after a single generation when estimates from this method are compared to prefragmentation estimates, given data for ~20 microsatellite loci in samples of 50 individuals. We consider a range of loci (10–40) and individuals (25–100) typical of current studies of natural populations and show that increasing the number of loci gives nearly the same increase in precision as increasing the number of individuals sampled. We also evaluated effects of incomplete fragmentation and found this N _e-reduction signal is still apparent in the presence of considerable migration (m ~ 0.10–0.25). Single-sample genetic estimates of N _e thus show considerable promise for early detection of population fragmentation and decline.     

Patterns of differentiation among endangered pondberry populations

Pondberry, Lindera melissifolia, is an endangered and partially clonally reproducing shrub species found in isolated populations that inhabit seasonally wet depressions in forested areas of the lower Mississippi River alluvial valley and southeastern regions of the United States. With eleven microsatellite loci, we quantified population genetic differentiation and diversity among 450 genets in 10 locations distributed across pondberry’s range. We used estimates of F _st and Jost’s D _est to measure genetic differences between populations and between geographic regions. The largest pairwise regional difference was found between eastern and western regional population groups (F _st = 0.23, D _est = 0.67), with the northern-most population groups in each region exhibiting larger divergence from each other than the southern-most population groups. Genetic diversity was lowest in the Sand Pond Conservation Area (A _e = 1.9, H _e = 0.36), which was the northern-most pondberry population, and highest in the Francis Marion National Forest (A _e = 4.1, H _e = 0.69), although we identified only 17 genets in that admixed population. Following adjustments for estimated null allele frequencies, we identified heterozygote excess in four eastern populations and found no evidence for inbreeding in any population. The observed patterns of differentiation indicate a phylogeography that exhibits an Appalachian Mountain discontinuity coupled with northward migrations along the Southern Atlantic Coastal Plain and into the Mississippi Alluvial Plain. The genetic consequences of this proposed phylogeographical structure may affect selection of germplasm sources for population reestablishment programs across pondberry’s range.     

Effective size of density‐dependent two‐sex populations: the effect of mating systems

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N_e in short‐lived, density‐dependent animal populations with different mating systems. We study the impact of a fluctuating, density‐dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N_e/N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male‐biased, density‐dependent sex ratio reduces the rate of genetic drift compared to an equal, density‐independent sex ratio, but a stochastic change towards male bias reduces the N_e/N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes.     

Genetic differences between continuous and disjunct populations: some insights from sal (<Emphasis Type="Italic">Shorea robusta</Emphasis> Roxb.) in Nepal

Sal (Shorea robusta Gaertn., Dipterocarpaceae) is a wind-pollinated tropical tree species found in southern Asia. We investigated the genetic diversity and structure at four microsatellites of 15 populations comprising continuous-peripheral and disjunct-peripheral populations in Nepal. Estimates of genetic diversity (N _A = 8.98, H _O = 0.62, H _E = 0.69) were similar when compared with those of other tropical tree species. A higher level of genetic diversity was observed in continuous-peripheral populations (N _A = 9.61, H _O = 0.67, H _E = 0.72) as compared to disjunct-peripheral (N _A = 8.04, H _O = 0.55, H _E = 0.64). Population differentiation was higher among disjunct-peripheral populations (F _ST = 0.043) than among continuous peripherals (F _ST = 0.012). There was a significant association between gene flow distances and genetic differentiation (r ² = 0.128, P ≤ 0.007). No spatial arrangement of populations according to their geographical locations was found. Based on observed genetic diversity protection of some populations in continuous-peripheral range are suggested for the sustainable conservation of genetic resources of the species while protection of some disjunct-peripheral populations are also recommended for conserving rare alleles.     

High genetic diversity with low connectivity among Mauritia flexuosa (Arecaceae) stands from Ecuadorean Amazonia

Mauritia flexuosa dominated palm swamps are an important forest resource covering over 30,000 km² across the Amazon basin. In Ecuadorean Amazonia, Mauritia flexuosa, a dioecious and arborescent palm species, forms small and isolated populations or large and dense stands on poorly drained soils. How these populations are genetically interconnected and how genetic diversity varies between cohorts of different ages remains little studied although they are important for conservation of these ecosystems. The genetic structure of Mauritia flexuosa was studied in five natural stands using eight microsatellite loci and two cohorts (seedling and adults). In addition, age structure and sex ratio within the stands were assessed using transects. The age structure of the studied Mauritia flexuosa stands is represented by a high number of seedlings (mean = 1,153.6/ha) and adults (mean = 563.2/ha), with a sex ratio favoring female individuals (1.42:1). These stands are also characterized by a fine‐scale genetic structure, high observed heterozygosity (mean: H_{O seedlings}=0.52; H_{O adults}=0.52), high inbreeding (mean: F_{IS seedlings} = 0.26; F_{IS adults} = 0.26), low number of migrants (N_m=0.29), strong genetic differentiation (mean: pairwise R_ST/ D‐values _seedlings = 0.08/ 0.74; mean R_ST/D‐values _adults = 0.17/ 0.76), and an average effective population size (N_e) of 191.42 individuals. No intergenerational genetic variation was detected between seedlings and adults. We suggest that the high genetic diversity and inbreeding as well as the strong differentiation among stands of these populations could be explained, at least partially, by a low genetic connectivity among populations. Destructive harvesting of its fruits and defaunation will be major threats to Mauritia flexuosa populations in the future. Abstract in Spanish is available with online material     

Spatial and temporal dynamics of the male effective population size in bumblebees (Hymenoptera: Apidae)

Eusociality and male haploidy of bumblebees (Bombus spp.) enhance the deleterious effects of population decline and aggravate the degeneration of population fitness compared to solitary and diploid species. The highly dispersive male sex may be the prime driver to connect otherwise isolated populations. We therefore studied the temporal and spatial structure of the male population of Bombus terrestris (Linnaeus 1758) and Bombus lapidarius (Linnaeus 1758) using microsatellite DNA markers. We found that the majority of the males in a 1000 m2 sampling area originated from colonies located outside of the workers foraging range, which was consistent with the genetic distances among colonies. The analyses of temporal population sub-structure based on both colony detection rate over time and the clustering software STRUCTURE consistently suggested one large and temporally unstructured male population. Our results indicate an extended male flight distance for both species. Though the range of queen dispersal remains to be studied, the effective size (N _e) of bumblebees is increased by extended male mating flight ranges (A _m ) exceeding worker foraging distance by factor 1.66 (A _m  = 69.75 km²) and 1.74 (A _m  = 13.41 km²), B. terrestris and B. lapidarius, respectively. Thus this behaviour may counteract genetic deprivation and its effects. All populations were genetically highly diverse and showed no signs of inbreeding. We discuss the implications of our findings in context of bumblebee population dynamics and conservation. We also highlight the effects and benefits of sampling both workers and males for population genetic studies.     

Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy (Engraulis encrasicolus)

It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths from Adriatic European anchovy (Engraulis encrasicolus), a fish with large census sizes that supports numerous local fisheries. Stocks have fluctuated greatly over the past few decades, and the Adriatic fishery collapsed in 1987. Our results show a significant reduction of mean genetic parameters as a consequence of the population collapse. In addition, estimates of effective population size (N_e) are much smaller than those expected in a fishes with large population census sizes (N_c). Estimates of N_e indicate low effective population sizes, even before the population collapse. The ratio N_e/N_e ranged between 10⁻⁶ and 10⁻⁸, indicating a large discrepancy between the anchovy gene pool and population census size. Therefore, anchovy populations may be more vulnerable to fishery effort and environmental change than previously thought.     

Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity

Evidence‐based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of ~25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na = 2.27, Ar = 2.24, H_e = 0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of ~30% from historical levels (Na = 3.36, Ar = 3.29, H_e = 0.63). Significant differentiation is seen between current and historical samples (F_ST = 0.156, P = 0.0315), and the current population exhibits extremely small N_e (current N_e = 2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical N_e = 1162.96). Individuals in the current population are related at the level of half‐ to full‐siblings between social groups, and full‐siblings or parent–offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential.     

Interannual variation in effective number of breeders and estimation of effective population size in long‐lived iteroparous lake sturgeon (Acipenser fulvescens)

Quantifying interannual variation in effective adult breeding number (N_b) and relationships between N_b, effective population size (N_e), adult census size (N) and population demographic characteristics are important to predict genetic changes in populations of conservation concern. Such relationships are rarely available for long‐lived iteroparous species like lake sturgeon (Acipenser fulvescens). We estimated annual N_b and generational N_e using genotypes from 12 microsatellite loci for lake sturgeon adults (n = 796) captured during ten spawning seasons and offspring (n = 3925) collected during larval dispersal in a closed population over 8 years. Inbreeding and variance N_b estimated using mean and variance in individual reproductive success derived from genetically identified parentage and using linkage disequilibrium (LD) were similar within and among years (interannual range of N_b across estimators: 41–205). Variance in reproductive success and unequal sex ratios reduced N_b relative to N on average 36.8% and 16.3%, respectively. Interannual variation in N_b/N ratios (0.27–0.86) resulted from stable N and low standardized variance in reproductive success due to high proportions of adults breeding and the species' polygamous mating system, despite a 40‐fold difference in annual larval production across years (437–16 417). Results indicated environmental conditions and features of the species' reproductive ecology interact to affect demographic parameters and N_b/N. Estimates of N_e based on three single‐sample estimators, including LD, approximate Bayesian computation and sibship assignment, were similar to annual estimates of N_b. Findings have important implications concerning applications of genetic monitoring in conservation planning for lake sturgeon and other species with similar life histories and mating systems.     

Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin

There is an increasing awareness that the long-term viability of endemic island populations is negatively affected by genetic factors associated with population bottlenecks and/or persistence at small population size. Here we use contemporary samples and historic museum specimens (collected 1888–1938) to estimate the effective population size (N _e) for the endangered yellow-eyed penguin (Megadyptes antipodes) in South Island, New Zealand, and evaluate the genetic concern for this iconic species. The South Island population of M. antipodes—constituting almost half of the species’ census size—is thought to be descended from a small number of founders that reached New Zealand just a few hundred years ago. Despite intensive conservation measures, this population has shown dramatic fluctuations in size over recent decades. We compare estimates of the harmonic mean N _e for this population, obtained using one moment and three likelihood based-temporal methods, including one method that simultaneously estimates migration rate. Evaluation of the N _e estimates reveals a harmonic mean N _e in the low hundreds. Additionally, the inferred low immigration rates (m = 0.003) agree well with contemporary migration rate estimates between the South Island and subantarctic populations of M. antipodes. The low N _e of South Island M. antipodes is likely affected by strong fluctuations in population size, and high variance in reproductive success. These results show that genetic concerns for this population are valid and that the long-term viability of this species may be compromised by reduced adaptive potential.