Habitat and diet of young grouse broods: resource partitioning between Capercaillie (Tetrao urogallus) and Black Grouse (Tetrao tetrix) in boreal forests

We compared habitat use and diets of young Capercaillie and Black Grouse broods in a boreal forest in southeast Norway. We used pointing dogs to search for broods (N = 83) in mature “natural” forest types and examined the crop content of 66 chicks 1–9 weeks old. We also measured the abundance of insects in the habitats where broods were found. Although overlapping substantially in both habitat and diets, there were notable differences: Capercaillie broods were more frequently recorded in bilberry-dominated forest types, whereas Black Grouse preferentially used pine bog forest, a more open habitat with little bilberry. Capercaillie chicks ate proportionally more insects, particularly lepidopteran larvae, and insects dominated their diet for a longer period of time (until age 28–29 days) than in Black Grouse (14–15 days). After reaching their peaks, the quantity of insects in the crops declined rapidly especially in Capercaillie, and in one of 2 years this occurred at a time when insects, including larvae, were still abundant in the habitats. Among plant foods, both species ate large amounts of Bilberry (Vaccinium myrtillus) and Bog Whortleberry (V. uliginosum). The main difference between species was a large proportion of both over-wintered and new, not yet ripe, berries of Cranberry (Oxycoccus quadripetalus) in Black Grouse, and a higher proportion of the forb Melampyrum sylvaticum in Capercaillie. The difference in diets reflected their differential use of habitats; the Vaccinium-preferred habitats of Capercaillie were richer in insects, particularly larvae, than the pine bog habitat preferred by Black Grouse. Because insects, especially larvae, comprised a larger proportion of the diet of Capercaillie chicks and chicks of this species need more food to sustain their rapid growth, Capercaillie is likely to be more sensitive to variation in insect food than Black Grouse. Also, by reducing the abundance of bilberry, the main host plant of larvae chick food, clearcutting forestry has negative effects on the brood habitat quality of both species.     

河北塞罕坝秋季黑琴鸡种群密度调查

2009年10月对河北塞罕坝地区的黑琴鸡(Lyrurus tetrix)秋季种群密度进行了专项集中调查。结果表明,秋季种群密度为2.20只/km2;与历史资料对比,该地区黑琴鸡种群密度呈明显下降趋势;种群分布发生了变化;繁殖基数、繁殖成功率下降和秋季猎捕是造成黑琴鸡秋季数量下降的主要因素。目前,加强管理、阻止盗猎活动是保护当地黑琴鸡种群的最有效措施。     

Estimating Effective Population Size from Temporally Spaced Samples with a Novel,Efficient Maximum-Likelihood Algorithm

The effective population size N_e is a key parameter in population genetics and evolutionary biology, as it quantifies the expected distribution of changes in allele frequency due to genetic drift. Several methods of estimating N_e have been described, the most direct of which uses allele frequencies measured at two or more time points. A new likelihood-based estimator NB^ for contemporary effective population size using temporal data is developed in this article. The existing likelihood methods are computationally intensive and unable to handle the case when the underlying N_e is large. This article tries to work around this problem by using a hidden Markov algorithm and applying continuous approximations to allele frequencies and transition probabilities. Extensive simulations are run to evaluate the performance of the proposed estimator NB^, and the results show that it is more accurate and has lower variance than previous methods. The new estimator also reduces the computational time by at least 1000-fold and relaxes the upper bound of N_e to several million, hence allowing the estimation of larger N_e. Finally, we demonstrate how this algorithm can cope with nonconstant N_e scenarios and be used as a likelihood-ratio test to test for the equality of N_e throughout the sampling horizon. An R package “NB” is now available for download to implement the method described in this article.     

Effective population size associated with self-fertilization: lessons from temporal changes in allele frequencies in the selfing annual Medicago truncatula

Despite its significance in evolutionary and conservation biology, few estimates of effective population size (N(e)) are available in plant species. Self-fertilization is expected to affect N(e), through both its effect on homozygosity and population dynamics. Here, we estimated N(e) using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated N(e) values were around 5-10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing N(e) estimates and levels of genetic variation suggest that H(e) is a poor estimator of the contemporaneous variance effective population size.     

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.     

Disentangling the impact of demographic factors on population differentiation of an endangered freshwater crayfish (Austropotamobius pallipes) using population density and microsatellite data

1. Habitat fragmentation of stream ecosystems often results in decreased connectivity between populations and lower population sizes. Hence, understanding how habitat fragmentation affects genetic erosion is important for the preservation of freshwater biodiversity, in particular, as small populations suffer from loss of genetic diversity through genetic drift and loss of fitness because of inbreeding, increasing the risk of extinction. 2. Here, we assess the impact of demographic factors on population differentiation in the endangered freshwater crayfish Austropotamobius pallipes by analysing population genetic structure, estimating effective population sizes and comparing levels of polymorphism at five microsatellite loci with density estimates of 10 populations within a small French catchment that has become progressively confined to headwaters over the last six decades. 3. Levels of expected heterozygosity and allelic richness per population were relatively low (0.214–0.396 and 1.6–2.6, respectively). We found strong genetic differentiation between these geographically close populations (F_ST = 0.283), with weak statistical evidence for a pattern of isolation by distance. Estimates of effective population size were low (<150) in most populations, but potentially reached several thousands in three populations. 4. Population density and allelic richness were strongly positively correlated. A robust relationship between population density and heterozygosity values was also noted, but only after discarding two populations for which significant genetic signatures of a recent bottleneck were found; these two populations displayed high expected heterozygosity compared with a very low density. Populations with the highest densities of individuals had the highest effective population size estimates and vice versa. 5. Our results clearly show the importance of demographic factors and genetic drift on A. pallipes populations. Furthermore, analysis of genetic and population density data is a pragmatic and efficient approach to corroborate inferences from genetic data and can be particularly useful in the identification of populations experiencing a bottleneck and therefore in conservation genetics studies aiming at identifying priority populations for conservation.     

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.     

managedpop: a computer simulation to project allelic diversity in managed populations with overlapping generations

We present a Monte Carlo simulation, managedpop , to project the loss of allelic diversity in a population with overlapping generations supported (or invaded) by a prodigious subpopulation. Input parameters allow the user to account for complex life histories and critical management practices, such as the frequency at which supportive breeding stocks are replaced. The simulation could also be used to examine the threat of species or population level extinction via hybridization. managedpop merges theoretical formulations on the effective size of supported populations and of populations with overlapping generations using easily measured life history traits.     

Effect of linkage on the control of inbreeding in selection programmes

Selection and mating methods for controlling inbreeding in selection programmes are based on relationships obtained from pedigrees. The efficiency of these methods has always been tested by studies using genetic models of independent loci. However, under linkage the rate of inbreeding obtained from pedigrees can be different from the probability of identity by descent of genes. We simulated a quantitative trait under artificial selection controlled by a large number of genes spread on genome regions of different sizes. A method to control inbreeding based on minimising the average coancestry of selected individuals with a restriction in the loss of selection response, and a mating procedure to control inbreeding were applied. These methods, that use coancestry relationships, were not effective in controlling inbreeding when the genome sizes were smaller than five morgans or so. However, for larger genome sizes the methods were sufficiently efficient. For very tight linkage, methods that utilise molecular information from markers should be used. We finally discuss the effects of the selection of individual major genes on the neutral variability of adjacent genome regions.     

Loss of genetic variability in a fragmented continuously distributed population

An individual-based simulation model was used to examine the effect of population subdivision, dispersal distance of offspring, and migration rates between subpopulations on genetic variability(H ₁ H _S andH _T ) in a continuously distributed population. Some difficulties with mathematical models of a continuously distributed population have been pointed out. The individual-based model can avoid these difficulties and can be used to examine genetic variability in a population within which individuals are distributed continuously and in which the dispersal of individuals is disturbed by geographical or artificial barriers. The present simulation showed that the pattern of decrease inH ₁ had three stages. During the first stage,H ₁ decreased at the rates predicted by Wright’s neighborhood size. During the second stage,H ₁ decreased more rapidly when the migration rate decreased, while during the third stage, it decreased less rapidly when the migration rate decreased. Increasing the number of subdivisions increased the rate of decrease after the 200th generation. The pattern of decrease inH _T was classified into 2 stages. During the first stage, the rates of decrease corresponded with those of a randomly mating population. During the second stage, a decrease in the migration rates of the subpopulations slowed the rate of decrease inH _T . A uniform spatial distribution and a reduced total dispersal distance of offspring causedH ₁ H _S , andH _T to decrease more rapidly. Habitat fragmentation in a continuously distributed population usually was detrimental to the genetic variability in the early generations. Other implications of the results for conservation are discussed.     

Common Buzzard (Buteo buteo): A raptor with hyperpolymorphic plumage morphs, but low allozyme heterozygosity

Summary The analysis of 25 allozyme loci in up to 469 Common Buzzards (B. b. buteo) from five locations in Germany revealed allelic polymorphism at twelve loci, but a prevalence of rare alleles resulted in a very low heterozygosity of H_o=0.0057. This rather low level of genetic variation characterizes a most abundant raptor species with highly polymorphic plumage pigmentation. The results of monitoring 571 buzzard breeding pairs from the Hakel forest (Sachsen-Anhalt) over 27 years indicate that neither the among-pair fertility variance, which slightly increased the genetically effective population size against the numerical size, nor the yearwise fluctuation of the breeder numbers, nor other population ecological characters were likely to erode the genetic variation of the numerically large buzzard population. One or repeated phyletic or historical bottle-necks are postulated to have diminished the allozyme variability, and at the same time to have created new genetic variance of the pigment-coding genes from non-additive components of genetic variance. Thus, the plumage colour diversity of the Common Buzzard could be a direct result of diminished single-locus genetic variation.

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Niedrige Enzym-Heterozygotie beim Mäusebussard (Buteo buteo buteo), einem Kulturfolger mit Farbphasen-Polymorphismus

Zusammenfassung Zwölf Alloyzm-Polymorphismen, aufgedeckt bei der enzym-elektrophoretischen Untersuchung von 25 erschlossenen Loci bei bis zu 469 Mäusebussarden (B. b. buteo) von fünf mitteleuropäischen Standorten, ergeben aufgrund des Vorherrschens seltener Allele eine niedrige biochemisch-genetische Heterozygotie von H_o=0.0057. Diese niedrige Mischerbigkeit betrifft einen häufigen Greifvogeln mit ausgeprägtem Farbphasen-Polymorphismus des Gefieders. Der Bruterfolg von 571 Bussardpaaren im Hakel (Sachsen-Anhalt), dokumentiert über 27 Jahre, erlaubt die Abschätzung einiger populationsgenetisch relevanter Kenngrößen der Bussardpopulation. Populationsökologische Einflüsse auf den genetischen Polymorphismus, soweit erfaßt, senken die genetisch effektive Populationsgröße der Art nicht hinreichend ab, um die niedrige Enzym-Heterozygotie erklären zu können. Historische Bestandesengpässe während der Radiation und Ausbreitung der artenreichen GattungButeo aus ihrem südamerikanischen Entstehungszentrum ins zoogeographisch terminal gelegene europäische Areal vonB. b. buteo, oder noch frühere Engpässe in der Phylogenie werden als hypothetische Ursache diskutiert. Die geringe Enzym-Heterozygotie und der auffällige Gefieder-Polymorphismus könnten in einem kausalen Zusammenhang stehen, sofern die Färbungsvariabilität auf nicht-additiver genetischer Varianz beruht. Diese kann bei Absenkung der Einzellocus-Varianz durch einen Populationsengpaß ansteigen.

     

Discrepancies in population differentiation at microsatellites, mitochondrial DNA and plumage colour in the pied flycatcher--inferring evolutionary processes

Genetic differentiation between three populations of the pied flycatcher Ficedula hypoleuca (Norway, Czech Republic and Spain, respectively) was investigated at microsatellite loci and mitochondrial DNA (mtDNA) sequences and compared with the pattern of differentiation of male plumage colour. The Czech population lives sympatrically with the closely related collared flycatcher (F. albicollis) whereas the other two are allopatric. Allopatric populations are on average more conspicuously coloured than sympatric ones, a pattern that has been explained by sexual selection for conspicuous colour in allopatry and a character displacement on breeding plumage colour in sympatry that reduces the rate of hybridization with the collared flycatcher. The Czech population was genetically indistinguishable from the Norwegian population at microsatellite loci and mtDNA sequences. Recent isolation and/or gene flow may explain the lack of genetic differentiation. Accordingly, different selection on plumage colour in the two populations is either sufficiently strong so that gene flow has little impact on the pattern of colour variation, or differentiation of plumage colour occurred so recently that the (presumably) neutral, fast evolving markers employed here are unable to reflect the differentiation. Genetically, the Spanish population was significantly differentiated from the other populations, but the divergence was much more pronounced at mtDNA compared to microsatellites. This may reflect increased rate of differentiation by genetic drift at the mitochondrial, compared with the nuclear genome, caused by the smaller effective population size of the former genome. In accordance with this interpretation, a genetic pattern consistent with effects of small population size in the Spanish population (genetic drift and inbreeding) were also apparent at the microsatellites, namely reduced allelic diversity and heterozygous deficiency.     

Small effective population sizes in a widespread selfing species, Lymnaea truncatula (Gastropoda: Pulmonata)

We present here a spatial and temporal population genetic survey of a common freshwater snail, also a predominantly selfing species, Lymnaea truncatula. The rate of genetic diversity loss was quantified by estimating the effective size (Ne) of the snail populations, using two different methods. A temporal survey allowed estimation of a variance effective size of the populations, and a spatial survey allowed the estimation of an inbreeding effective size, from two-locus identity disequilibria estimates. Both methods were consistent and provided low Ne values. Drift due to (i) high amounts of selfing and (ii) fluctuations in population sizes because of temporary habitats, and also selection coupled to genome-wide linkage disequilibria, could explain such reductions in Ne. The loss of genetic diversity appears to be counterbalanced only very partially by low apparent rates of gene flow.     

Spatio-temporal genetic variability in sea trout (Salmo trutta) populations from north-western Spain

1. Genetic variation at five microsatellite loci was investigated in six sea trout ( Salmo trutta ) populations to describe their spatio-temporal genetic variation in north-western Spain. We observed significant genetic variation between river basins, and isolation by distance with restricted gene flow between neighbouring rivers, which suggests an important homing behaviour.
2. Despite these populations suffering a serious demographic decline during 1998, we did not detect any reduction in their genetic variation, suggesting a reasonably high effective population size and temporal stability.
3. Genetic differences among rivers should be taken into account in future management activities. Given the high genetic variability and the temporal stability observed, we believe that no supportive breeding programmes are presently needed in these populations.     

Low genetic variability in a natural alpine marmot population (Marmota marmota, Sciuridae) revealed by DNA fingerprinting

Genetic heterogeneity is usually considered an important factor for the viability of a population, yet there are cases in which populations sustain themselves despite virtual homozygosity. A prior step to studying the effects of such low levels of genetic variability can be the analysis of its causes. We analysed a population of the highly social alpine marmot ( Marmota marmota , Sciuridae) by multilocus DNA fingerprinting. The fingerprint patterns revealed a very low degree of polymorphism in our main study population. We show that this lack of hypervariability is caused by a low effective population size, rather than by an unusual low mutation rate of the fingerprint loci studied. However, the current number of breeding pairs was found to be about an order of magnitude larger than the one that would be expected to lead to such a low degree of heterozygosity. We conclude that there must have been bottlenecks in the history of the Berchtesgaden marmot population that have severely affected its genetic heterozygosity.     

The efficiency of purifying selection in Mammals vs. Drosophila for metabolic genes

The nearly neutral theory of molecular evolution states that the efficiency of natural selection depends on the effective population size. By using a wide range of multispecies data on nucleotide polymorphism, we have tried to ascertain whether there are any differences in the level of selective constraints of metabolic process genes between Mammals and Drosophila species. The results are consistent with a higher selective constraint in Drosophila than in Mammals, according to the expected under the nearly neutral model: purifying selection seems to be more efficient in species with a larger effective population size.     

Genetic variability in the European bison (Bison bonasus) population from Białowieża forest over 50 years

The aim of this study was to assess potential post-bottleneck temporal genetic differentiation following the reintroduction of the species into the Białowieża Forest. Variability of 12 polymorphic microsatellite markers was analysed for 178 individuals born between 1955 and 2005, divided by birth year into five temporal groups. Low overall allelic richness (AR) per locus (AR = 2.0) and a low overall expected heterozygosity (H_E = 0.28) were observed. The overall F _IS was not significantly different from zero. The mean F _IS values were, however, significantly different from zero for individuals born between 1955 and 1965 ( F _IS = 0.19). A Bayesian computation was used to estimate effective population size (N_e) for each temporal group. We observed relatively small values of N_e ranging from 7.9 to 28.4. The low N_e values confirm that, despite a rapid growth of the bison population following the founder event, N_e increased only slowly.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 801–809.     

Microgeographical breeding structure of the tsetse fly, Glossina pallidipes in south-western Kenya

The origins of extant Glossina pallidipes Austen (Diptera: Glossinidae) populations in the ecologically well-studied Lambwe and Nguruman valleys in Kenya are controversial because populations have recovered after seemingly effective attempts to achieve high levels of control. The microgeographical breeding structure of the tsetse fly, G. pallidipes, was investigated by analysing spatial and temporal variation at eight microsatellite loci to test hypotheses about endemism and immigration. Samples were obtained at seasonal intervals from trap sites separated by 200 m to 14 km and arranged into blocks. G. pallidipes populations nearest to Lambwe and Nguruman also were sampled. Spatial analysis indicated that genetic differentiation by genetic drift was much less among trapping sites within Lambwe and Nguruman (F(ST) < or = 0.049) than between them (F(ST) = 0.232). F(ST) between Serengeti and Nguruman was 0.16 and F(ST) between Kodera Forest and Lambwe was 0.15. The genetic variance in G. pallidipes explained by dry and wet seasons (0.33%) was about one-fifth the variance among collection dates (1.6%), thereby indicating reasonable temporal stability of genetic variation. Gene frequencies in Kodera and Serengeti differed greatly from Lambwe and Nguruman, thereby falsifying the hypothesis that Lambwe and Nguruman were repopulated by immigrants. Harmonic mean effective (= breeding) population sizes were 180 in Lambwe and 551 in Nguruman. The genetic data suggest that G. pallidipes in Lambwe and Nguruman have been endemic for long intervals.     

DNA “fingerprinting” and the genetic management of a captive chimpanzee population (Pan troglodytes)

DNA fingerprinting probes are cloned sequences which simultaneously detect a large number of similar hypervariable loci in the target DNA. The resulting highly polymorphic pattern visualized on an autoradiograph allows resolution of questions concerning individual identification and parentage. M13 bacteriophage has been used as a DNA fingerprinting probe for paternity ascertainment among captive chimpanzees housed in multi-male groups as part of the National Chimpanzee Breeding and Research Program. In 31 cases of unknown paternity where DNA samples for mother, offspring, and all potential sires were available, DNA fingerprinting with M13 resulted in the unambiguous assignment of paternity for all 31 infants. Knowledge of pedigrees among the captive-born animals is used to address several issues important in the genetic management of captive breeding colonies, including estimation of effective population size and of the rate of decline in genetic variability, variance in male and female reproduction, and the effect of social dominance on male reproductive success. Our analysis demonstrates the beneficial effects of genetic management by comparing the managed dedicated cohort to the Bastrop colony as a whole.