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The long-term persistence of a population which has suffered a bottleneck partly depends on how historical demographic dynamics impacted its genetic diversity and the accumulation of deleterious mutations. Here we provide genomic evidence for the detrimental genetic effect of a recent population bottleneck in the endangered black-faced spoonbill (Platalea minor) even after its rapid population recovery. Our population genomic data suggest that the bird’s effective population size, N, had been relatively stable (7,500-9,000) since the end of the last glacial maximum; however, a recent brief yet severe bottleneck (N= 20) around the 1940s wiped out more than 99% of its historical N in roughly three generations. By comparing it with its sister species, the royal spoonbill (P. regia) whose conservation status is of lesser concern, we found that despite a more than 15-fold population recovery since 1988, genetic drift has led to higher levels of inbreeding (7.4 times more runs of homozygosity longer than 100 Kb) in the black-faced spoonbill than in the royal spoonbill genome. Although the two spoonbills have similar levels of genome-wide nucleotide diversity and heterozygosity, because of relaxed purifying selection, individual black-faced spoonbills carry 3% more nonsynonymous substitutions than royal spoonbills each of which is 7% more deleterious. Our results imply that the persistence of a threatened species cannot be inferred from a recovery in its population. They also highlight the necessity of continually using genomic indices to monitor its genetic health and employing all possible measures to assure its long-term persistence in the ever-changing environment.

Demographic bottlenecks generally reduce genetic diversity through more intense genetic drift, but their net effect may vary along the genome due to the random nature of genetic drift and to local effects of recombination, mutation, and selection. Here, we analyzed the changes in genetic diversity following a bottleneck by comparing whole-genome diversity patterns in populations with and without severe recent documented declines of Iberian (Lynx pardinus, n = 31) and Eurasian lynx (Lynx lynx, n = 29). As expected, overall genomic diversity correlated negatively with bottleneck intensity and/or duration. Correlations of genetic diversity with divergence, chromosome size, gene or functional site content, GC content, or recombination were observed in nonbottlenecked populations, but were weaker in bottlenecked populations. Also, functional features under intense purifying selection and the X chromosome showed an increase in the observed density of variants, even resulting in higher θW diversity than in nonbottlenecked populations. Increased diversity seems to be related to both a higher mutational input in those regions creating a large collection of low-frequency variants, a few of which increase in frequency during the bottleneck to the point they become detectable with our limited sample, and the reduced efficacy of purifying selection, which affects not only protein structure and function but also the regulation of gene expression. The results of this study alert to the possible reduction of fitness and adaptive potential associated with the genomic erosion in regulatory elements. Further, the detection of a gain of diversity in ultra-conserved elements can be used as a sensitive and easy-to-apply signature of genetic erosion in wild populations.

International audience; The Mascarene Petrel Pseudobulweria aterrima is a critically endangered seabird endemic to Reunion Island, with an extremely small population suffering several threats. Fifteen polymorphic microsatellite loci were isolated from this species to analyse genetic diversity, estimate contemporary effective population size, search for evidence of a population bottleneck and see whether results support the hypothesis that life history traits could preserve allelic diversity in small populations. Results from 22 individuals found grounded as a consequence of light pollution highlight a surprisingly high genetic diversity, an absence of inbreeding, a contemporary effective population size estimated at approximately 1211 individuals and a probable bottleneck around 10 000 generations ago. Additional studies on genetic diversity and structure from a larger number of samples are thus required to evaluate the evolutionary potential of this critically endangered species.

Genetic diversity is important for long‐term viability of a population. Low genetic diversity reduces persistence and survival of populations and increases susceptibility to diseases. Comparisons of the neutral markers with functional loci such as immune genes [Toll‐like receptors; TLR] can provide useful insights into evolutionary potential of a species and how the diversity of pathogens and selection pressures on their hosts are directly linked to their environment. In this study, we compare genetic diversity in neutral (eleven microsatellite loci) and adaptive (seven TLR loci) loci to determine genetic variation in a nonmigratory western Himalayan passerine, the black‐throated tit (Aegithalos concinnus), distributed across an elevation gradient with varying degree of pathogen‐mediated selection pressure. We further compare the diversity in TLR loci with a high‐elevation sister species, the white‐throated tit (Aegithalos niveogularis). Our results indicate a lack of population genetic structure in the black‐throated tit and signatures of a past bottleneck. In contrast, we found high diversity in TLR loci and locus‐specific (TLR7) signatures of pathogen‐mediated selection, which was comparable to diversity in the white‐throated tit. Levels of diversity at TLR5 locus corresponded very closely with neutral microsatellite variation. We found evidence of positive selection in TLR1LA, TLR5, and TLR7 loci highlighting the importance in pathogen recognition. Our finding demonstrates that reduction in neutral variation does not necessarily lead to reduction in functional genetic diversity and probably helps in revival of population in a widespread species., Comparisons of allelic richness (size corrected) using eight neutral loci and seven TLR loci (*p

A pivotal debate on biodiversity conservation is whether the scarce budgets must be invested in critically endangered taxa or in those with higher chances to survive due to larger population sizes. Addressing the fate of extremely bottlenecked taxa is an ideal way to test this idea, but empirical cases are surprisingly limited. The reintroduction of the extinct-in-the-wild Alagoas curassow (Pauxi mitu) by Brazilian scientists in September 2019 added to the two other known cases of survival to bottlenecks of only two or three individuals. We exploit the reasons why this species has survived, and we report how investments to rescue the Alagoas curassow resulted in the protection of many other taxa, suggesting that in the face of the dramatic number of extinctions expected for the Anthropocene, integration must prevail over a choice.

The evolutionary trajectory of populations through time is influenced by the interplay of forces (biological, evolutionary, and anthropogenic) acting on the standing genetic variation. We used microsatellite and mitochondrial loci to examine the influence of population declines, of varying severity, on genetic diversity within two Hawaiian endemic waterbirds, the Hawaiian coot and Hawaiian gallinule, by comparing historical (samples collected in the late 1800s and early 1900s) and modern (collected in 2012–2013) populations. Population declines simultaneously experienced by Hawaiian coots and Hawaiian gallinules differentially shaped the evolutionary trajectory of these two populations. Within Hawaiian coot, large reductions (between −38.4% and −51.4%) in mitochondrial diversity were observed, although minimal differences were observed in the distribution of allelic and haplotypic frequencies between sampled time periods. Conversely, for Hawaiian gallinule, allelic frequencies were strongly differentiated between time periods, signatures of a genetic bottleneck were detected, and biases in means of the effective population size were observed at microsatellite loci. The strength of the decline appears to have had a greater influence on genetic diversity within Hawaiian gallinule than Hawaiian coot, coincident with the reduction in census size. These species exhibit similar life history characteristics and generation times; therefore, we hypothesize that differences in behavior and colonization history are likely playing a large role in how allelic and haplotypic frequencies are being shaped through time. Furthermore, differences in patterns of genetic diversity within Hawaiian coot and Hawaiian gallinule highlight the influence of demographic and evolutionary processes in shaping how species respond genetically to ecological stressors.

Dispersal is a process that increases genetic diversity and genetic connectivity of populations. We studied the turnover rate of breeding adults and genetic population structure to estimate dispersal in Peregrine Falcons in Finland. We used relatedness estimates among Finnish Peregrine Falcons over a 5-year period, genotyping over 500 nestlings with 10 microsatellite loci to reveal the rate of turnover. Our results reveal a high turnover rate (21.7%) that does not seem to be correlated with the breeding success of the previous year. The extent of population genetic structure and diversity, and possible signs of the population crash during the 1970s, was assessed with a reduced dataset, excluding relatives. We found genetic diversity to be similar to previously studied falcon populations (expected heterozygosity of 0.581) and no population genetic structuring among our sampled populations. We did not find a genetic imprint of the past population bottleneck that the Finnish Peregrine population experienced. We conclude that high dispersal rates are likely to have contributed to maintaining genetic diversity across the landscape, by mixing individuals within the species' distribution in Finland and thus preventing genetic structuring and negative effects associated with the population decline in the 1970s. (Less)

The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long-term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 264 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance-based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 50.38% success rate in species recovery (133/264), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α-diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β-diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi-marker metabarcoding approaches and tailor-made (i.e., order-specific) taxonomic delimitation thresholds.

A relationship between winter weather and survival of northern ungulates has long been established, yet the possible roles of biological (e.g., nutritional status) and environmental (e.g., weather) conditions make it important to determine which potential limiting factors are most influential.Our objective was to examine the potential effects of individual (body mass and age) and extrinsic (winter severity and snowmelt conditions) factors on the magnitude and timing of mortality for adult (>2.5 years old) female white‐tailed deer (Odocoileus virginianus [Zimmerman, 1780]) during February–May in the Upper Peninsula of Michigan, USA.One hundred and fifty deer were captured and monitored during 2009–2015 in two areas with varying snowfall. February–May survival ranged from 0.24 to 0.89 (mean = 0.69) across years. Mortality risk increased 1.9% with each unit increase in cumulative winter severity index, decreased 8.2% with each cumulative snow‐free day, and decreased 4.3% with each kg increase in body mass. Age and weekly snow depth did not influence weekly deer survival. Predation, primarily from coyote (Canis latrans [Say, 1823]) and wolves (Canis lupus [L., 1758]), accounted for 78% of known‐cause mortalities.Our results suggest that cumulative winter severity, and possibly to a lesser degree deer condition entering winter, impacted deer winter survival. However, the timing of spring snowmelt appeared to be the most influential factor determining late‐winter mortality of deer in our study. This supports the hypothesis that nutrition and energetic demands from weather conditions are both important to northern ungulate winter ecology. Under this model, a delay of several weeks in the timing of spring snowmelt could exert a large influence on deer survival, resulting in a survival bottleneck., Northern ungulate population dynamics are correlated with winter weather patterns, and our goal was to evaluate when and why white‐tailed deer winter mortality occurs. We modeled weekly mortality risk of 150 adult female white‐tailed deer in Michigan in response to environmental and biological factors. The results suggested that body mass, severity of winter weather, and timing of spring snowmelt are influential on deer mortality, with the timing of snowmelt explaining the greatest amount of variation.

The excessive commercial collection of matsutake mushrooms can lead to extreme reduction of population size, which may cause genetic bottleneck and decrease genetic diversity of Tricholoma matsutake. Here, six polymorphic microsatellite loci markers were used to examine the genetic diversity of four natural T. matsutake populations from two main producing regions of China. The minimum combinations of four loci were able to discriminate total 86 sampled individuals with distinctive multilocus genotypes. Our analysis of molecular variance (AMOVA) revealed that about 80% and 20% of the overall genetic variation were respectively partitioned within and among populations. The principal-coordinate analyses (PCA) distinguished the four tested populations into three genetic clusters, each of which was correlated with respective endemic host plants on a geographical basis. The AMOVA, PCA and pairwise population FST estimates consistently displayed the same genetic divergence patterns and spatial structure of T. matsutake mediated by host plants in China. The significant heterozygosity excesses demonstrated that a recent genetic bottleneck occurred in each population tested. The complementary M-ratio test indicated past genetic bottleneck events over longer periods. Only four individuals were identified as putative first generation migrants within northeastern China, which implies restricted interpopulation gene flow in T. matsutake. We discuss that the significant genetic differentiation among populations of T. matsutake is most likely a function of host adaptation, host specificity, genetic bottleneck, limited dispersal and habitat fragmentation.

Summary Signal transduction processes are typically initiated by the interaction of signal molecules with sensor domains. The current lack of information on the signal molecules that feed into regulatory circuits forms a major bottleneck that hampers the understanding of regulatory processes. McKellar et al. report a high-throughput approach for the identification of signal molecules, which is based on thermal shift assays of recombinant sensor domains in the absence and presence of compounds from commercially available ligand collections. Initial binding studies with the sensor domain of the PctA chemoreceptor of Pseudomonas aeruginosa showed a close match between thermal shift assay results and microcalorimetric studies reported previously. Using thermal shift assays the authors then identify signals that bind to three chemoreceptors of the kiwifruit pathogen P. syringae pv. Actinidiae NZ-V13. Microcalorimetric binding studies and chemotaxis assays have validated the relevance of these ligands. The power of this technique lies in the combination of a high-throughput analytical tool with commercially available compound collections. The approach reported is universal since it can be employed to identify signal molecules to any type of sensor domain. There is no doubt that this technique will facilitate the identification of many signal molecules in future years.

Accounting for historical demographic features is vital for many types of evolutionary inferences, including the estimation of divergence times between closely related populations. In barn swallow, Hirundo rustica, inferring historical population sizes and subspecies divergence times can shed light on the recent co-evolution of this species with humans. Pairwise sequentially Markovian coalescent uncovered population growth beginning on the order of one million years ago-which may reflect the radiation of the broader Hirundo genus-and a more recent population decline. Additionally, we used approximate Bayesian computation to evaluate hypotheses about recent timescale barn swallow demography, including population growth due to human commensalism, and a potential founder event associated with the onset of nesting on human structures. We found signal for a bottleneck event approximately 7,700 years ago, near the time that humans began building substantial structures, although there was considerable uncertainty associated with this estimate. Subspecies differentiation and subsequent growth occurred after the bottleneck in the best-supported model, an order of magnitude more recently than previous estimates in this system. We also compared results obtained from whole-genome sequencing versus reduced representation sequencing, finding many similar results despite substantial allelic dropout in the reduced representation data, which may have affected estimates of some parameters. This study presents the first genetic evidence of a potential barn swallow founder effect and subspecies divergence coinciding with the Holocene, which is an important step in analysing the biogeographical history of a well-known human commensal species.

The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.

Spatial and environmental heterogeneity are major factors in structuring species distributions in alpine landscapes. These landscapes have also been affected by glacial advances and retreats, causing alpine taxa to undergo range shifts and demographic changes. These nonequilibrium population dynamics have the potential to obscure the effects of environmental factors on the distribution of genetic variation. Here, we investigate how demographic change and environmental factors influence genetic variation in the alpine butterfly Colias behrii. Data from 14 microsatellite loci provide evidence of bottlenecks in all population samples. We test several alternative models of demography using approximate Bayesian computation (ABC), with the results favouring a model in which a recent bottleneck precedes rapid population growth. Applying independent calibrations to microsatellite loci and a nuclear gene, we estimate that this bottleneck affected both northern and southern populations 531-281 years ago, coinciding with a period of global cooling. Using regression approaches, we attempt to separate the effects of population structure, geographical distance and landscape on patterns of population genetic differentiation. Only 40% of the variation in F(ST) is explained by these models, with geographical distance and least-cost distance among meadow patches selected as the best predictors. Various measures of genetic diversity within populations are also decoupled from estimates of local abundance and habitat patch characteristics. Our results demonstrate that demographic change can have a disproportionate influence on genetic diversity in alpine species, contrasting with other studies that suggest landscape features control contemporary demographic processes in high-elevation environments.

We use a branching process approach to estimate the substitution rate, the rate at which beneficial mutations occur and fix, in populations of lytic viruses whose growth is controlled by periodic population bottlenecks. Our model predicts that substitution rates, and by extension adaptation rates, are profoundly affected by the survival of infected host cells at the bottleneck. In particular, we find that direct transfer (or environmental) bottlenecks, in which some fraction of both free virus and host cells are preserved, are associated with relatively slow adaptation rates for the virus. In contrast, viruses can adapt much more quickly when only free virus is transferred to a new host population, as is typical in an epidemiological setting. Finally, when premature lysis of the host-cell population is induced at the bottleneck, we predict that adaptation rates for the virus will, in general, be faster still. These results hold irrespective of the life-history trait affected by the beneficial mutation. The substitution rates in the presence of environmental bottlenecks are predicted to be as much as an order of magnitude lower than in the other two cases.

The analysis of molecular data from natural populations has allowed researchers to answer diverse ecological questions that were previously intractable. In particular, ecologists are often interested in the demographic history of populations, information that is rarely available from historical records. Methods have been developed to infer demographic parameters from genomic data, but it is not well understood how inferred parameters compare to true population history or depend on aspects of experimental design. Here we present and evaluate a method of SNP discovery using RNA-sequencing and demographic inference using the program δaδi, which uses a diffusion approximation to the allele frequency spectrum to fit demographic models. We test these methods in a population of the checkerspot butterfly Euphydryas gillettii. This population was intentionally introduced to Gothic, Colorado in 1977 and has since experienced extreme fluctuations including bottlenecks of fewer than 25 adults, as documented by nearly annual field surveys. Using RNA-sequencing of eight individuals from Colorado and eight individuals from a native population in Wyoming, we generate the first genomic resources for this system. While demographic inference is commonly used to examine ancient demography, our study demonstrates that our inexpensive, all-in-one approach to marker discovery and genotyping provides sufficient data to accurately infer the timing of a recent bottleneck. This demographic scenario is relevant for many species of conservation concern, few of which have sequenced genomes. Our results are remarkably insensitive to sample size or number of genomic markers, which has important implications for applying this method to other non-model systems.

The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk analysis, then examine evidence for the importance of specific processes maintaining the bottleneck using the multiple competing hypotheses approach, and finally integrate these results through a sensitivity analysis of a demographic model using life-stage simulation analysis (LSA) to determine the relative importance of genetic, demographic, environmental, and catastrophic processes on population growth. Annual population growth has been slow and variable (1.0 ± 5.2 parrots per year, or an average λ = 1.05 ± 0.19) from 16 parrots (1973) to a high of 40–42 birds (1997–1998). A risk analysis based on population prediction intervals (PPI) indi...

Although most natural populations are genetically subdivided, they are often analysed as if they were panmictic units. In particular, signals of past demographic size changes are often inferred from genetic data by assuming that the analysed sample is drawn from a population without any internal subdivision. However, it has been shown that a bottleneck signal can result from the presence of some recent immigrants in a population. It thus appears important to contrast these two alternative scenarios in a model choice procedure to prevent wrong conclusions to be made. We use here an Approximate Bayesian Computation (ABC) approach to infer whether observed patterns of genetic diversity in a given sample are more compatible with it being drawn from a panmictic population having gone through some size change, or from one or several demes belonging to a recent finite island model. Simulations show that we can correctly identify samples drawn from a subdivided population in up to 95% of the cases for a wide range of parameters. We apply our model choice procedure to the case of the chimpanzee (Pan troglodytes) and find conclusive evidence that Western and Eastern chimpanzee samples are drawn from a spatially subdivided population.

The adoption of self-fertilization from an ancestral outcrossing state is one of the most common evolutionary transitions in the flowering plants. In the mustard family, outcrossing is typically enforced by sporophytic self-incompatibility (SI), but there are also many self-compatible species. The genus Leavenworthia contains taxa that either possess or lack SI. Here, we present data showing that SI is associated with strict outcrossing and that there is widespread trans-specific sequence polymorphism at the locus involved in the recognition of self-pollen (the S-locus). This ancestral polymorphism is consistent with the presence of an outcrossing mating system in the common ancestor of Leavenworthia species, and suggests that there have been several independent losses of SI in the group. When compared with other mustard species, the bulk of Leavenworthia S-allele sequences are highly diverged from those found in other Brassicaceae and show relatively low levels of nucleotide diversity, a pattern that suggests the common ancestor of the genus likely underwent a strong population bottleneck. The hypothesis of postbottleneck S-locus rediversification is supported by tests showing stronger positive selection acting on S-alleles from Leavenworthia than those found in other Brassicaceae.

Range expansion and contraction has occurred in the history of most species and can seriously impact patterns of genetic diversity. Historical data about range change are rare and generally appropriate for studies at large scales, whereas the individual pollen and seed dispersal events that form the basis of geneflow and colonization generally occur at a local scale. In this study, we investigated range change in Fagus sylvatica on Mont Ventoux, France, using historical data from 1838 to the present and approximate Bayesian computation (ABC) analyses of genetic data. From the historical data, we identified a population minimum in 1845 and located remnant populations at least 200 years old. The ABC analysis selected a demographic scenario with three populations, corresponding to two remnant populations and one area of recent expansion. It also identified expansion from a smaller ancestral population but did not find that this expansion followed a population bottleneck, as suggested by the historical data. Despite a strong support to the selected scenario for our data set, the ABC approach showed a low power to discriminate among scenarios on average and a low ability to accurately estimate effective population sizes and divergence dates, probably due to the temporal scale of the study. This study provides an unusual opportunity to test ABC analysis in a system with a well-documented demographic history and identify discrepancies between the results of historical, classical population genetic and ABC analyses. The results also provide valuable insights into genetic processes at work at a fine spatial and temporal scale in range change and colonization.

Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and Approximate Bayesian Computation, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important problems in conservation and evolutionary biology.

It is well known that standard population genetic theory predicts decreased additive genetic variance (V(a) ) following a population bottleneck and that theoretical models including interallelic and intergenic interactions indicate such loss may be avoided. However, few empirical data from multicellular model systems are available, especially regarding variance/covariance (V/CV) relationships. Here, we compare the V/CV structure of seventeen traits related to body size and composition between control (60 mating pairs/generation) and bottlenecked (2 mating pairs/generation; average F = 0.39) strains of mice. Although results for individual traits vary considerably, multivariate analysis indicates that V(a) in the bottlenecked populations is greater than expected. Traits with patterns and amounts of epistasis predictive of enhanced V(a) also show the largest deviations from additive expectations. Finally, the correlation structure of weekly weights is not significantly different between control and experimental lines but correlations between necropsy traits do differ, especially those involving the heart, kidney and tail length.

The degree to which historical human activities negatively impacted past and present lemur species is a long-standing question in primatology. At present, most evidence addressing this issue comes from archaeology, paleontology, and behavioral studies. Genetic data provide another source of evidence. In this study, six microsatellite loci, genotyped on more than 360 wild Verreaux’s sifaka, are used in order to test the hypothesis that this population experienced a population bottleneck in the last 2000 years. Excess heterozygosity is compared with the heterozygosity expected under mutation-drift equilibrium in order to test for the genetic signature of a rapid population contraction in the past. The results indicate that the sifaka population did not experience a population bottleneck. Various methodological and conceptual implications of this result are discussed. Am. J. Primatol. 70:990–994, 2008. c 2008 Wiley-Liss, Inc.

The bottleneck model proposed by Powell1 can describe the growth rate hysteresis effect, but fails to account for the stationary state of microbial cultures. It is modified to obtain an extended bottleneck model (EBM), which adequately represents the stationary state of microbial cultures. The basis for modification is the metabolic turnover of proteins in microorganisms. Under special conditions the EBM can be reduced to the Powell bottleneck model or the Monod model. The EBM yields improved predictions of the transient growth of E. coli in nitrogen limited cultures.

We have estimated the extent of genetic variation in museum (1890s) and contemporary (1980s) samples of Florida panthers Puma concolor coryi for both nuclear loci and mtDNA. The microsatellite heterozygosity in the contemporary sample was only 0.325 that in the museum samples although our sample size and number of loci are limited. Support for this estimate is provided by a sample of 84 microsatellite loci in contemporary Florida panthers and Idaho pumas Puma concolor hippolestes in which the contemporary Florida panther sample had only 0.442 the heterozygosity of Idaho pumas. The estimated diversities in mtDNA in the museum and contemporary samples were 0.600 and 0.000, respectively. Using a population genetics approach, we have estimated that to reduce either the microsatellite heterozygosity or the mtDNA diversity this much (in a period of c. 80 years during the 20th century when the numbers were thought to be low) that a very small bottleneck size of c. 2 for several generations and a small effective population size in other generations is necessary. Using demographic data from Yellowstone pumas, we estimated the ratio of effective to census population size to be 0.315. Using this ratio, the census population size in the Florida panthers necessary to explain the loss of microsatellite variation was c. 41 for the nonbottleneck generations and 6.2 for the two bottleneck generations. These low bottleneck population sizes and the concomitant reduced effectiveness of selection are probably responsible for the high frequency of several detrimental traits in Florida panthers, namely undescended testicles and poor sperm quality. The recent intensive monitoring both before and after the introduction of Texas pumas in 1995 will make the recovery and genetic restoration of Florida panthers a classic study of an endangered species. Our estimates of the bottleneck size responsible for the loss of genetic variation in the Florida panther completes an unknown aspect of this account.

In the ecological stoichiometry theory of population dynamics, ontogenetic changes in nutrient demand have been ignored. Here, I studied a stage-structured Daphnia–algae herbivore–autotroph model, in which the juveniles of the herbivore had a higher nutrient (phosphorous) demand for maturation than the adults for reproduction. The model predicted that while an increase in the juvenile nutrient demand (i.e., ontogenetic stoichiometric bottleneck) affects stage-specific performances in complex ways through nutrient dynamics and resource quality, in general it has stabilizing effects on the population dynamics.

Knowledge about the variability spectra of neutrally evolving sequences in a population is a prerequisite for the identification of genes, which may have been under positive selection during recent human evolution. Here, we report the results of a re-sequencing project of a presumably neutrally evolving chromosome 22 locus with a severely reduced recombination frequency in a group of 24 individuals of German origin. The comparison of these data with the results of a similar analysis of a chromosome 17 locus revealed striking differences, although the same group of individuals was used. For the chromosome 17 locus two well-separated groups of sequences, a positive value of Tajima's D and a TMRCA of 700,000 years were observed. In contrast, the sequences from the chromosome 22 locus were found to be relatively homogeneous, with no deep splits between subgroups; the obtained value for Tajima's D was negative and the TMRCA was only 260,000 years. These discrepancies may be explained by selection or demographic processes. Regarding demography, the most plausible explanation is the assumption of a severe bottleneck in the history of the European population: in the case of the chromosome 17 locus two ancient lineages passed this bottleneck; for the chromosome 22 locus it was only one ancient lineage.

Previous research showed that the Choctaw Indians of Oklahoma exhibit considerable linkage disequilibria (LD) in a number of regions of the genome that has allowed genetic fine mapping for potential susceptibility genes for the autoimmune connective tissue disease scleroderma, or systemic sclerosis (SSc). In principle, such enhanced background LD in the Choctaws could be caused by population bottleneck event(s) followed by recent population expansion. This investigation utilizes genome-scan data on 175 dinucleotide loci from 76 Choctaw individuals to seek genetic evidence of the demographic history of the Choctaw Nation. Of the 175 loci examined, 105 are in Hardy-Weinberg equilibrium. The average unbiased homozygosity over the 105 loci for the Choctaws (29.3%) is significantly higher than that in the European descent group (20.9%); and when adjusted for sample-size differences, the Choctaw also exhibit a significantly smaller number of segregating alleles (6.65 vs. 8.14) at these loci. Both of these observations are consistent with the trend expected in an isolated population. Comparison of the allele size variance and gene diversity yields an imbalance index (lnbeta) of 0.811 in the Choctaw. Of the 105 loci examined, 93 exhibit excess expected homozygosity in comparison to the expectations of a stepwise mutation model in a population of constant size. Taken together, these observations are consistent with a signature of the recent population size expansion of the Choctaws, preceded by bottleneck event(s).

G protein-coupled receptors (GPCRs) are an important, medically relevant class of integral membrane proteins. Laboratories throughout all disciplines of science devote time and energy into developing practical methods for the discovery, isolation, and characterization of these proteins. Since the crystal structure of rhodopsin was solved 6 years ago, the race to determine high-resolution structures of more GPCRs has gained momentum. Since certain GPCRs are currently produced at sufficient levels for X-ray crystallography trials, it is speculated that heterologous expression of GPCRs may no longer be a bottleneck in obtaining crystal structures. This Review focuses on the current approaches in heterologous expression of GPCRs and explores the problems associated with obtaining crystal structures from GPCRs expressed in different systems. Although milligram amounts of certain GPCRs are attainable, the majority of GPCRs are still either produced at very low levels or not at all. Developing reliable expression techniques for GPCRs is still a major priority for the structural characterization of GPCRs.

International audience; Genome wide patterns of nucleotide diversity and recombination reveal considerable variation including hotspots. Some studies suggest that these patterns are primarily dictated by individual locus history related at a broader scale to the population demographic history. Because bottlenecks have occurred in the history of numerous species, we undertook a simulation approach to investigate their impact on the patterns of aggregation of polymorphic sites and linkage disequilibrium (LD). We developed a new index (Polymorphism Aggregation Index) to characterize this aggregation and showed that variation in the density of polymorphic sites results from an interplay between the bottleneck scenario and the recombination rate. Under particular conditions, aggregation is maximized and apparent mutation hotspots resulting in a 50-fold increase in polymorphic sites density can occur. In similar conditions, long distance LD can be detected.

The northern elephant seal (NES) suffered a severe population bottleneck towards the end of the nineteenth century. Theoretical expectations for the impact of population bottlenecks include the loss of genetic diversity and a loss of fitness (e.g. through a disruption of developmental stability); however, there are few direct demonstrations in natural populations. Here, we report on the comparison of archive samples collected prior to and following the NES population bottleneck. Measures of genetic diversity show a loss of variation consistent with expectations and suggest a strong disruption in the pattern of allele frequencies following the bottleneck. Measures of bilateral characters show an increase in fluctuating asymmetry.

Peregrine falcon populations underwent devastating declines in the mid-20th century due to the bioaccumulation of organochlorine contaminants, becoming essentially extirpated east of the Great Plains and significantly reduced elsewhere in North America. Extensive re-introduction programs and restrictions on pesticide use in Canada and the United States have returned many populations to predecline sizes. A proper population genetic appraisal of the consequences of this decline requires an appropriate context defined by (i) meaningful demographic entities; and (ii) suitable reference populations. Here we explore the validity of currently recognized subspecies designations using data from the mitochondrial control region and 11 polymorphic microsatellite loci taken from 184 contemporary individuals from across the breeding range, and compare patterns of population genetic structure with historical patterns inferred from 95 museum specimens. Of the three North American subspecies, the west coast marine subspecies Falco peregrinus pealei is well differentiated genetically in both time periods using nuclear loci. In contrast, the partitioning of continental Falco peregrinus anatum and arctic Falco peregrinus tundrius subspecies is not substantiated, as individuals from these subspecies are historically indistinguishable genetically. Bayesian clustering analyses demonstrate that contemporary genetic differentiation between these two subspecies is mainly due to changes within F. p. anatum (specifically the southern F. p. anatum populations). Despite expectations and a variety of tests, no genetic bottleneck signature is found in the identified populations; in fact, many contemporary indices of diversity are higher than historical values. These results are rationalized by the promptness of the recovery and the possible introduction of new genetic material.

Potential variability in nutrient limitation among tree size classes, functional groups and species calls for an integrated community- and ecosystem-level perspective of lowland tropical rainforest nutrient limitation. In particular, canopy trees determine ecosystem nutrient conditions, but competitive success for nutrients and light during the sapling bottleneck determines canopy composition. We conducted an in situ multi-nutrient sapling fertilization experiment at La Selva Biological Station, Costa Rica, to determine how functional group identity, species identity and light availability can impact nutrient limitation of stem growth in three functional groups and nine species. Despite high soil fertility, we found nutrient-light limitation in two functional groups and four species. Unexpectedly, the nitrogen-fixing (“N2 fixers”) and shade-tolerant functional groups were significantly nutrient limited, while the light-demanding functional group was not. This was partially explained by species-level variation in nutrient limitation within these functional groups, with only some species conforming to the prediction of stronger nutrient limitation in light demanders compared to shade-tolerants. Most surprisingly, we found strong nutrient limitation at low-light levels in the N2 fixers (which were shade-tolerant), but not in the shade-tolerant non-fixers. We hypothesize that the N2 fixers were actually nitrogen limited at low-light levels because of their nitrogen-rich leaves and the high carbon cost of their symbionts. This finding suggests a highly shade-tolerant, N2 fixation strategy, in addition to the perception that N2 fixation is mostly advantageous in high-light environments during early and gap succession. The shade-tolerant, N2 fixation strategy may be part of a sapling and canopy tree feedback, where the canopy N2 fixers enrich the soil N, enhancing growth of their shade-tolerant saplings relative to non-fixing competitors, enabling further canopy domination by shade-tolerant N2 fixers, as seen at La Selva. Synthesis. The pervasiveness of functional group- and species-specific nutrient and light co-limitation in our saplings indicates that these interactions likely play an important role in the dynamics of lowland tropical rainforest nutrient limitation, potentially via other such sapling and canopy tree feedbacks as the one hypothesized.

Over the last century, populations of the Greater Prairie Chicken ( Tympanuchus cupido ) have de- clined or gone extinct throughout midwestern North America. In Wisconsin the population declined by 50% from 1951 to 1961 and has remained at low (1500 individuals) but fluctuating levels for the past 40 years. We examined historic (1951) and contemporary (1996-1999) populations of prairie chickens in Wisconsin to determine whether there was a loss of genetic variation following the population bottleneck. We compared microsatellite DNA variation at six loci in historic (1951, n � 47) and contemporary (1996-1999, n � 87) populations. Population mean heterozygosity and number of alleles per locus were significantly lower in the late 1990s than in 1951. This loss of genetic variation following a population bottleneck is consistent with the results of a similar study in Illinois, but we found no evidence of a reduction in hatching success.

We found evidence for a critical population bottleneck at a developmental-stage transition in larvae of the zebra mussel Dreissena polymorpha Pallas from field estimates of mortality. Identification of this critical period in the field was made possible by closely tracking cohorts of larvae over 5 days of development as they dispersed 128 km in a river system. The presence of a survival bottleneck during development was confirmed in laboratory studies of zebra mussel larvae. Development-specific mortality has important implications for spatial population dynamics of the zebra mussel in particular, and all species with indirect development in general. Marine reserves that do not take development-specific mortality into account may dramatically underestimate reserve size needed to protect rare and/or exploited marine populations. Conversely, for the zebra mussel, the lower contribution of dispersing individuals to population growth downstream of reserves can lead to more feasible control through the blocking of dispersal.

Commercial exploitation reduced the North Atlantic right whale (Eubalaena glacialis) population from c. 12 000 in the 11th century to around 300 by the 21st century. We examine the effect of this population decline on levels of genetic variation at 16 microsatellite loci and contrast levels of variability to that in a closely related species (E. australis). Of the 13 loci developed from the E. glacialis genome, 100% were polymorphic in E. australis. In contrast, nine loci were polymorphic in E. glacialis and four were fixed. Both allelic diversity (A) and heterozygosity (H) were significantly lower in E. glacialis than E. australis (A = 3.2 ± 2.6 vs. A= 6.9 ± 3.3, P

13 pages; International audience; Understanding what factors determine the success of an invasive species in its adopted range is crucial from an evolutionary ecology point of view, because it can provide insights into which biological characteristics are required for survival in varied environmental conditions. Successful establishment may depend on both maintaining genetic diversity, which will allow the species to evolve and/or adapt to new environments, and the presence or absence of natural enemies such as parasites. We tested these two hypotheses by studying populations of the amphipod crustacean Dikerogammarus villosus . This Ponto-Caspian invader has rapidly and successfully invaded western Europe and threatens macroinvertebrate biodiversity in its adopted ranges. It is a unique system to study since both its colonisation history and its geographic origins are well-known. Using samples from the whole geographic range of the invasion route, and using four molecular markers, we found no evidence for genetic bottlenecks during the invasion of D. villosus in western Europe, despite slight variations in allelic proportions according to spatio-temporal subdivisions of our dataset. In addition, we analysed the prevalence and diversity of parasites across its native and adopted range. We found no macro-parasites, and no significant parasite loss of microsporidian parasites during the invasive process. Our data suggest that D. villosus invasion was either massive, or recurrent, or both, allowing a parasitic cortege to follow the host. The maintenance of genetic diversity may have contributed to its success, including the variation in resistance in the face of the natural enemies.

Population bottlenecks reduce genetic diversity and thus cause great concern in conservation biology. Previous theoretical studies often assume discrete generations in projecting declines in genetic diversity caused by bottlenecks. This assumption creates complexities when applying the models to long-lived species with overlapping generations. bottlesim is a program for simulating bottlenecks to estimate the impact on genetic diversity; the novelties include an overlapping-generation model, a wide range of reproductive systems, and flexible population size settings. With these features, bottlesim will be a useful tool for estimating the genetic consequences of bottlenecks, evaluating conservation plans, and performing power analysis.

The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe population crash associated with an increase in alien ungulate populations on Mauna Kea, and a population bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the population bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the population bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the population bottleneck of at most three individuals. The results suggest that: (i) small populations, even those that result from severe reductions in historical population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.

The Whooping Crane (Grus americana) is an endangered bird that suffered a severe population bottleneck; only 14 adults survived in 1938. We assessed the genetic effect of this human-caused bottleneck by sequencing 314 base pairs ( bp) of the mitochondrial DNA control region from cranes that lived before, during, and after this bottleneck. The maximum length of DNA amplifiable from museum specimens was negatively correlated with age, and only 10 of 153 specimens yielded the entire 314 bp sequence. Six haplotypes were present among the prebottleneck individuals sequenced, and only one of these persists in the modern population. The most common modern haplotype was in low frequency in the prebottleneck population, which demonstrates the powerful effect of genetic drift in changing allele frequencies in very small populations. By combining all available data, we show that no more than one-third of the prebottleneck haplotypes survived the human-caused population bottleneck. High levels of variation of substitution rates among nucleotide sites prevented us from estimating the prebottleneck population size. Our data will be incorporated into the captive breeding program to allow better management decisions regarding the preservation of current genetic diversity. These data offer the first glimpse into the genetic toll this species has paid for human activities. Resumen: La Grulla Americana (Grus americana) es un ave amenazada que sufrio un cuello de botella poblacional severo con tan solo 14 adultos sobreviviendo en 1938. Evaluamos el efecto genetico de este cuello de botella causado por humanos secuenciando 314 pb de la region control del ADN mitocondrial de grullas que vivieron antes, durante y despues de este cuello de botella. La longitud maxima de ADN amplificable de especimenes de museo estuvo negativamente correlacionada con la edad, y solo 10 (de 153) especimenes produjeron la secuencia completa con los 314 pb. Cinco haplotipos estuvieron presentes entre los individuos pre-cuello de botella secuenciados y solo uno de estos persiste en las poblaciones modernas. El haplotipo moderno mas comun era de baja frecuencia en la poblacion pre-cuello de botella, lo cual demuestra el poderoso efecto de la deriva genica en frecuencias cambiantes de alelos en poblaciones muy pequenas. Al combinar todos los datos a la mano, mostramos que no mas de una tercera parte de los haplotipos pre-cuello de botella sobrevivieron a un cuello de botella ocasionado por humanos. Los altos niveles de la tasa de variacion entre sitios, impidio la estimacion del tamano poblacional previo al cuello de botella. Nuestros datos pueden ser incorporados al programa de reproduccion en cautiverio para permitir decisiones de manejo mejor enfocadas para la preservacion de la diversidad genetica actual. Estos datos ofrecen un primer vistazo a el precio genetico que esta especie ha pagado debido a actividades humanas.

Traditional models of genetic drift predict a linear decrease in additive genetic variance for populations passing through a bottleneck. This perceived lack of heritable variance limits the scope of founder-effect models of speciation. We produced 55 replicate bottleneck populations maintained at two male-female pairs through four generations of inbreeding (average F = 0.39). These populations were formed from an F2 intercross of the LG/J and SM/J inbred mouse strains. Two contemporaneous control strains maintained with more than 60 mating pairs per generation were formed from this same source population. The average level of within-strain additive genetic variance for adult body weight was compared between the control and experimental lines. Additive genetic variance for adult body weight within experimental bottleneck strains was significantly higher than expected under an additive genetic model This enhancement of additive genetic variance under inbreeding is likely to be due to epistasis, which retards or reverses the loss of additive genetic variance under inbreeding for adult body weight in this population. Therefore, founder-effect speciation processes may not be constrained by a loss of heritable variance due to population bottlenecks.

Monitoring temporal changes in genetic variation can provide estimates of effective population size ( Ne ) that are useful for detecting population bottlenecks. We used Monte Carlo computer simulations to quantify the bias and precision of the Ne estimates obtained from temporal changes in allele frequencies at allozyme and microsatellite loci. The estimates of Ne overestimated the true Ne by 12–200% after 1–10 generations of a bottleneck of effective size 4. This magnitude of bias, however, is not likely to cause bottlenecks to go undetected or to cause misguided management recommendations. The bias was nearly negligible for bottlenecks of effective size ≥10, until approximately five bottleneck generations had passed. Three causes of the bias are the loss of alleles, the assumption that the increase in variance in allele frequencies with time is additive (instead of multiplicative), and the assumption that selfing can occur when it cannot. We derived a new equation that substantially reduces the bias. The precision of Ne estimates was sufficient that, when true Ne was 4, the 95% confidence interval bracketing a Ne estimate was

The high prevalence of rare genetic diseases in Finland has been attributed to a founder effect some 2,000 years ago. However, this hypothesis has not been supported from mtDNA sequence and autosomal microsatellite data which indicate high levels of gene diversity. Here we have identified genetic evidence for a population bottleneck by examining variable microsatellite loci on the nonrecombining portion of Y chromosomes from Finland and four populations from Europe and the Americas. Sequence data from segment I of the control region (HVS-1) of mtDNA (360 bases) and 20 autosomal dinucleotide repeat markers were also analyzed. Partitions of genetic variance within and between populations revealed significant levels of Y-chromosome differentiation between populations. Phylogenetic and diversity analyses revealed divergent Finnish Y-haplotype clades and significantly lower Y-haplotype diversity among Finns as compared to other populations. Surprisingly, Finnish Y-haplotype diversity was even lower than the Native American populations. These results provide support for the Finnish bottleneck hypothesis. Evidence for two separate founding Finnish Y-chromosome lineages was also observed from the Y-chromosome phylogeny. A limited number of closely related founding males may have contributed to the low number of paternal lineages in the Finnish population. In contrast, high levels of genetic diversity for mtDNA and autosomal STRs may be the result of sex-biased gene flow and recent immigration to urban areas from established internal isolates within Finland. Am J Phys Anthropol 108:381–399, 1999. Published 1999 Wiley-Liss, Inc.

Summary 1. When prey occur at high densities, energy assimilation rates are generally constrained by rates of digestion rather than by rates of collection (i.e. search and handle). As predators usually select patches containing high prey densities, rates of digestion will play an important role in the foraging ecology of a species. 2. The red knot Calidris canutus shows tremendous inter- and intra-individual variation in maximum rates of digestion due to variation in the size of the processing machinery (gizzard and intestine), which makes it a suitable species to study the effects of digestive processing rate on foraging decisions. 3. Here we report on patch use, prey choice, and daily foraging times as a function of gizzard size in free-ranging, radio-marked, red knots. As knots crush their bulky bivalve prey in their gizzard, the size of this organ, which we measured using ultrasonography, determines digestive processing rate. 4. Using the digestive rate model, we a priori modelled patch use, prey choice, and daily foraging times as a function of gizzard mass. Focusing on two contrasting patches, birds with small gizzards were expected to feed on high-quality (soft-bodied) prey found in low densities in the one patch, while birds with large gizzards were expected to feed on low-quality (hard-shelled) prey found in high densities in the other patch. Assuming that red knots aim to balance their energy budget on a daily basis, we expected daily foraging time to decline with gizzard mass. 5. Observed patch and prey choices were in quantitative agreement with these theoretical predictions. Observed daily foraging times were only in qualitative agreement: they declined with gizzard mass but less steeply than predicted. 6. We discuss that red knots might be aiming for a slightly positive energy budget in order to (i) refuel their stores depleted during migration, and (ii) to insure against unpredictability in supply and demand during winter. Red knots arriving from their breeding grounds with small gizzards are only able to realize this aim when densities of soft-bodied prey are high, which is the case in late July and early August. Rapidly declining soft-bodied prey densities throughout late summer pose a major penalty for individuals arriving late at their wintering grounds. 7. The long daily foraging periods required by knots with small gizzards are only feasible through ‘tide-extension’. In our study area, birds can and do raise the daily low tide period from 12 h to almost 17 h by moving along with the tide in an easterly direction, subsequently flying back to their starting point at the high tide roost.

Summary 1. Rate-maximizing foragers that only divide their time between searching and handling prey should, according to the classical contingency model (CM), only select those prey whose energy content per unit handling time (i.e. profitability) exceeds or equals long-term average energy intake rate. 2. However, if digestively constrained foragers were to follow this so-called ‘zero-one rule’, they would need to take digestive breaks and their energy intake over total time would not be maximized. They should, according to the digestive rate model (DRM), also consider the rate at which a prey type is digested (i.e. digestive quality), such that time lost to digestive breaks is minimized. 3. In three different contexts, we tested these competing models in a mollusc-eating shorebird, the red knot ( Calidris canutus ), that is often digestively constrained due to its habit of ingesting its bulky prey whole. Measurements on gizzard size (using ultrasonography) and prey-characteristics confirmed that in each test the birds were digestively bottlenecked and should thus follow the DRM in order to maximize long-term energy intake. 4. In the first experiment, knots were offered a choice between two fully exposed prey, and tended to select prey by the criterion of digestive quality rather than profitability. 5. In the second experiment, knots were offered two buried prey types and preferred the highest quality prey to the most profitable prey. 6. In the wild, knots mainly fed on high quality Mya and largely ignored poor quality, but equally profitable, Cerastoderma . 7. Thus, each test verified the predictions of the DRM and rejected those of the CM. Given that many species face digestion constraints, we expect that the DRM is likely to explain diet composition in many more studies.

Summary 1 The Mauritius kestrel Falco punctatus (Temminck 1823) has recovered from very low numbers. In order to evaluate the severity of the population bottleneck that it experienced, we have developed a method for estimating the productivity of the nests that escaped detection. This method uses ringing records for MCMC estimation of parameters describing the recruitment of adults to the breeding population and the growth in productivity of undiscovered nests.2 Comparison of the estimates for the two restored populations (eastern and western) showed a far lower proportion of undiscovered nests in the former, as predicted because of widespread use of nestboxes. This served to verify the method of estimation. The estimates show a steady increase in population size, in contrast with field estimates indicating a recent reduction in growth.3 The results suggest that the alarmingly low estimates of population size in 1974 (two breeding pairs) were accurate, and that few undiscovered nests existed during the bottleneck.4 The recovery of the population seems to have been initiated by the intensive conservation effort. The most rapid period of population growth coincides with the reintroduction programme. The results imply that the eastern population is much more reliant on intensive management for its future growth.

We investigated the genetic consequences of a single-founder bottleneck in a population of showy Indian clover (Trifolium amoenum), a species presumed to be extinct until rediscovered near Occidental, California, in 1993. Electrophoretic variation was evaluated in the bottlenecked population and in a larger population (Dillon Beach) discovered during the course of this study, as well as in populations of two closely related species, T. albopurpureum var. dichotomum and T. macraei .W e found a surprisingly high amount of polymorphism in the single-founder T. amoenum population from Occidental (15% of loci polymorphic; an average of 1.1 alleles per locus). However, this represents a 53% reduction in number of polymorphic loci and a 20% reduction in average number of alleles per locus compared to three Trifolium populations with putatively similar mating systems (the Dillon Beach T. amoenum population and both populations of T. albopurpureum var. dichotomum). Expanding the genetic base of the Occidental T. amoenum population is a priority due to concerns about loss of evolutionary potential and the possibility of deleterious effects associated with inbreeding. However, using seed from the Dillon Beach T. amoenum population may not be beneficial due to distinct, presumably adaptive differences between plants from the two populations and concerns about outbreeding depression.

The endangered Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense) has experienced a severe decline in distribution and abundance because of predation by alien ungulates. By the late 1970s only a small remnant natural population persisted on the Mauna Kea volcano on the Island of Hawaii. The Hawaii Department of Land and Natural Resources, Division of Forestry and Wildlife, initiated an outplanting program in the 1970s to promote recovery of A. sandwicense ssp. sandwicense. Intermittent outplanting since 1973 has generated an outplanted population of over 450 plants on Mauna Kea, but the program has unintentionally resulted in a major population bottleneck. All plants in the outplanted population appear to be first- or subsequent-generation offspring of only two maternal founders from the natural population. Genetic variation in the natural and outplanted populations was assessed for 90 random amplified polymorphic DNA loci. Eleven loci were detectably polymorphic in the natural population, whereas only three loci were detectably polymorphic in the outplanted population. Thus, the population bottleneck has been accompanied by a 73% reduction in the level of detectable polymorphism. In addition, for eight loci, the population bottleneck has resulted in the loss of the marker allele in the outplanted population. A management strategy involving manual pollen transfer has recently been implemented to incorporate additional founders from the natural population into the outplanting program. As a supplement to the outplanting program, the strategy also includes a program promoting direct seedling establishment following manual pollen transfer. Incorporating additional founders may serve to overcome the legacy of the population bottleneck, especially if founder representation can be equalized. La Espada Plateada de Mauna Kea (Argyroxiphium sandwicense ssp. sandwicense) esta en peligro de extincion debido a una severa declinacion de su distribucion y abundancia en tiempos historicos causada por la depredacion de ungulados introducidos. A fines de la decada de 1970 solo persistia una pequena poblacion natural en el volcan Mauna Kea en la Isla de Hawaii. Tambien en esa decada el Departamento de Tierras y Recursos Naturales de Hawaii, por medio de la Division de Bosques y Vida Silvestre, inicio un programa de siembra para promover la recuperacion de Argyroxiphium sandwicense ssp. sandwicense. La siembra intermitente desde 1973 ha generado una poblacion de mas de 450 plantas en Mauna Kea. Sin embargo el programa de siembra, aunque sin intencion, ha resultado en un gran cuello de botella poblacional. Todas las plantas en la poblacion sembrada parecen ser la primera o subsecuentes generaciones de descendientes de solo dos fundadores maternos de la poblacion natural. Se determino la variacion genetica para 90 loci de ADN polimorficos amplificados en la poblacion natural y la sembrada. Once loci fueron marcadamente polimorficos en la poblacion natural, mientras que solo tres lo fueron en la poblacion sembrada. Por tanto, el cuello de botella poblacional esta acompanado por una reduccion del 73% en el nivel de polimorfismo detectable. Adicionalmente, el cuello de botella poblacional ha resultado en la perdida del alelo marcador para ocho loci en la poblacion sembrada. Recientemente se ha instrumentado una estrategia de manejo que involucra la transferencia manual de polen para incorporar fundadores adicionales de la poblacion natural al programa de siembra. Como un suplemento del programa de siembra, la estrategia tambien incluye un programa que promueve el establecimiento directo de plantulas despues de la transferencia manual de polen. La incorporacion de fundadores adicionales puede servir para superar el legado del cuello de botella, especialmente si la representacion de fundadores se equilibra.