Severe Bottleneck Research Articles

Nelson A. Rockefeller’s Office of Inter-American Affairs (1940-1946) and Record Group 229

Nelson A. Rockefeller’s Office of Inter-American Affairs (1940-1946) and Record Group 229

Inferring the Demographic History and Rate of Adaptive Substitution in Drosophila

An important goal of population genetics is to determine the forces that have shaped the pattern of genetic variation in natural populations. We developed a maximum likelihood method that allows us to infer demographic changes and detect recent positive selection (selective sweeps) in populations of varying size from DNA polymorphism data. Applying this approach to single nucleotide polymorphism data at more than 250 noncoding loci on the X chromosome of Drosophila melanogaster from an (ancestral) African population and a (derived) European, we found that the African population expanded about 60,000 y ago and that the European population split off from the African lineage about 15,800 y ago, thereby suffering a severe population size bottleneck. We estimated that about 160 beneficial mutations (with selection coefficients s between 0.05% and 0.5%) were fixed in the euchromatic portion of the X in the African population since population size expansion, and about 60 mutations (with s around 0.5%) in the diverging European lineage.

The myth of accelerating business processes through parallel job designs

This paper discusses postulated advantages of parallel job designs compared with sequential designs in business processes. Until now, the literature suggests an overall dominance of parallel designs. An analysis of relevant application domains, in which parallel tasks are prevalent in order to accelerate processes, offers two remarkable insights: (1) parallel tasks can but do not have to speed-up business processes; (2) coordination efforts may reduce or even invert potential performance gains. Thus, this paper thoroughly evaluates interdependencies between parallel designs and coordination efforts through simulation experiments. Several process patterns for order processing in a real-world example will be examined. The results offer noteworthy characteristics of parallel designs which extent the existing knowledge: (a) gains from parallelization are reduced with increasing process variability, (b) small increments in coordination efforts neutralize gains from parallelization, (c) in high work load situations, the resource capacity for the coordination task is a severe bottleneck, and (d) if the findings (a)–(c) are carefully considered, only the parallelization of multiple tasks leads to significant performance gains.

Decreased immunocompetence in a severely bottlenecked population of an endemic New Zealand bird

AbstractInbreeding resulting from severe population bottlenecks may impair an individual's immune system and render it more susceptible to disease. Although a reduced immune response could threaten the survival of highly endangered species, few studies have assessed the effect of population bottlenecks on immunocompetence. We compared the counts of leucocytes and external, blood and gastrointestinal parasite loads in two populations of the endemic New Zealand robin Petroica australis to assess the immunocompetence of birds in a severely bottlenecked population relative to its more genetically diverse source population. Despite similar parasite loads in both populations, robins in the severely bottlenecked population showed lower counts of both total leucocyte and total lymphocyte numbers. When the immune system was experimentally challenged using the phytohaemagglutinin skin test, robins in the severely bottlenecked population exhibited a significantly lower immune response than the source population, suggesting that birds passing through a severe bottleneck have a compromised immunocompetence. Our results confirm that severe bottlenecks reduce the immune response of birds and highlight the need to avoid severe bottlenecks in the recovery programmes of endangered species.

Phylogeography of the capercaillie in Eurasia: what is the conservation status in the Pyrenees and Cantabrian Mounts?

The Western capercaillie (Tetrao urogallus) is a keystone species of Palearctic boreal and altitude coniferous forests. With the increase of mountain leisure activities and habitat loss, populations are declining in most mountain ranges in Western Europe. Recent work has shown that the populations from the Pyrenees and Cantabrian Mountains survived a severe bottleneck during the 19th century, and are still considered as threatened due to habitat fragmentation and isolation with other populations. We present an extensive phylogeographic study based on mitochondrial DNA sequence (control region) extracted non-invasively from faeces collected throughout the species range (from western European mountains to central and eastern Europe, Fenno-Scandia, Russia and Siberia). We also compared our results with DNA sequences of closely related black-billed capercaillie (T. parvirostris). We found that populations from Pyrenees and Cantabrians are closely related but are different from all other capercaillie populations that form a homogenous clade. Therefore, we consider that these South-Western populations should be considered as forming an Evolutionary Significant Unit that needs an appropriate management at a local scale. We also discuss the possible locations of glacial refugia and subsequent colonisation routes in Eurasia, with a Western “aquitanus” lineage from Iberia and Balkans, and an Eastern “urogallus” lineage from Southern Asia. This work might have important implication for capercaillie conservation strategies to define important areas for conservation, and to prevent possible exchange or introductions of individuals originated from other lineages.

Genetic consequences of a demographic bottleneck in the Scandinavian arctic fox

Demographic bottlenecks can result in a loss of genetic variation due to the bottleneck effect and subsequent genetic drift. The arctic fox population in Scandinavia went through a severe demographic bottleneck in the early 20th century, and is today classified as critically endangered. In this study, we investigated the pre‐bottleneck genetic variation in Scandinavia and compared it to modern samples from Scandinavia and North Russia. Variation in the mtDNA control region and five microsatellite loci was examined through ancient DNA analysis on museum specimens. The microsatellite data from the museum specimens was further used to simulate the expected effect of the bottleneck. The arctic foxes in Scandinavia have lost approximately 25% of the microsatellite alleles and four out of seven mtDNA haplotypes. The results also suggest that the genetic differentiation between North Russia and Scandinavia has doubled over the last 100 years. However, the level of heterozygosity was significantly higher than expected from the simulations. This highlights both the advantage of using museum specimens and the importance of generating specific predictions in conservation genetics.

Distribution and genetic divergence of two parapatric sibling ant species in Central Europe

The two sibling ant species Temnothorax nylanderi and Temnothorax crassispinus are widely distributed throughout deciduous forests in Europe. Their resemblance in morphology and similar ecological requirements suggest that they evolved from the same ancestral species in different glacial refugia and re-immigrated into Central Europe after the last ice age. Here, we show that the two species are parapatrically distributed in south-eastern Germany and hybridize along a narrow contact zone close to the continental divide. Phylogeographical data based on the mitochondrial genes cytochrome oxidase subunit I and cytochrome b suggest that the dominant haplotypes for T. nylanderi and T. crassispinus might have diverged already 1.5–2 Mya. Intraspecific variability is extremely low in both species, which might be explained by severe bottlenecks during rapid postglacial expansion into Central Europe.

Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.

Genome-wide nucleotide variation in non-African populations of Drosophila melanogaster is a subset of variation found in East sub-Saharan African populations, suggesting a bottleneck in the history of the former. We implement an approximate Bayesian approach to infer the timing, duration, and severity of this putative bottleneck and ask whether this inferred model is sufficient to account for patterns of variability observed at 115 loci scattered across the X chromosome. We estimate a recent bottleneck 0.006N(e) generations ago, somewhat further in the past than suggested by biogeographical evidence. Using various proposed statistical tests, we find that this bottleneck model is able to predict the majority of observed features of diversity and linkage disequilibrium in the data. Thus, while precise estimates of bottleneck parameters (like inferences of selection) are sensitive to model assumptions, our results imply that it may be unnecessary to invoke frequent selective sweeps associated with the dispersal of D. melanogaster from Africa to explain patterns of variability in non-African populations.

Invasion success despite reduction of genetic diversity in the European populations of eastern mosquitofish (Gambusia holbrooki)

The introduction of a few individuals to new, isolated habitats (founder effect) is expected to reduce the genetic variability of a population. At the beginning of the last century a few eastern mosquitofish (Gambusia holbrooki) individuals were introduced to Southern Europe from North America to control malaria‐carrying mosquitoes. We studied the effect of this severe bottleneck on genetic variability in four populations of eastern mosquitofish introduced to Spain and Italy in the early 1900s and compared them to a native population in North America. Using amplified polymorphic DNA–polymerase chain reaction (RADP–PCR) we found a strong reduction of genetic diversity, in terms of both number of polymorphic loci and heterozygosity, in all four European populations. Despite this great reduction in genetic diversity, eastern mosquitofish successfully invaded European internal waters causing eutrophication problems and threatening the extinction of local populations of native fish.

Genetic variability and phylogenetic relationships of Cnemidophorus parecis (Squamata, Teiidae) from Cerrado isolates in southwestern Amazonia

We investigated the genetic structure of Cnemidophorus parecis, and its phylogenetic relationships with other South American teiids using allozyme data. Because of southward expansion of Amazon Forest, populations of C. parecis presumably have been isolated in Cerrado enclaves during the last 3000 years. We scored 18 presumptive electrophoretic loci in Tupinambis merianae, Kentropyx altamazonica, Ameiva ameiva, Cnemidophorus ocellifer, and C. parecis, estimating genetic diversity through allelic richness, mean number of alleles per locus, proportion of polymorphic loci, and mean heterozygosity. To make interspecific comparisons independent of sample sizes, we also used a rarefaction analysis of allelic richness. C. parecis had relatively low values of genetic variability among the five studied species, but the results do not corroborate the hypothesis that enclave populations experienced a severe bottleneck. Therefore, geographic isolation affected the genetic variability of C. parecis, but Rondônia enclaves were apparently large enough to maintain adequate populations of this species, preserving some of the original genetic diversity. We also conducted a phylogenetic analysis adding data from Cnemidophorus lemniscatus and Cnemidophorus gramivagus previously reported in literature and using T. merianae as outgroup. Results indicated that C. parecis is more closely related to A. ameiva than to other congeneric species, corroborating the view that South American Cnemidophorus form a paraphyletic assemblage.

Genetic diversity and geographic pattern of wild lotus (Nelumbo nucifera) in Heilongjiang Province

Based on 47 accessions from Ussuri River Valley, Songhua River Valley and Heilong River Valley together with 2 accessions from Russia and 27 accessions of cultivated lotus from other provinces in China, genetic diversity of wild lotus (Nelumbo nucifera) were revealed using RAPD and ISSR markers. Twenty RAPD primers generated 113 loci, of which 71.68% were polymorphic across all samples. The expected heterozygosity was 0.1583. The percentage of polymorphic loci and expected heterozygosity in the wild lotus were 50.44% and 0.1241, respectively. The parameters of the cultivated lotus were slightly higher, 53.98% and 0.1651 correspondingly. Sixteen ISSR primers produced 90 loci. The percentages of polymorphic loci and expected heterozygosity were 41.11% and 0.0851 at species level, 28.89% and 0.0661 for the wild lotus, and 32.22% and 0.0963 for the cultivated lotus. AMOVA analysis of the wild lotus showed that a small number of variances exist among the 3 river valleys (21.68% for RAPD with Gst=0.1312 and 15.11% for ISSR with Gst=0.1352). The molecular variances of both the wild and the cultivated lotuses came predominantly from within the 3 river valleys and the cultivated samples (73.25% for RAPD and 81.11% for ISSR). Variance components from the wild and the cultivated lotus accounted for 19.17% for RAPD and 13.17% for ISSR, and variations among the valleys and the culta seemed the least important (7.585 for RAPD and 5.725 for ISSR). Neighbor-joining analysis demonstrated that considerable differentiation happened between the wild and the cultivated lotus. The wild lotus at middle reaches of the Songhua River Valley seemed to be the centre of remnants, from which it spread to the Ussuri River Valley and the Heilong River Valley. The very limited genetic diversity suggests that the wild lotus has experienced severe bottleneck effect, founder effect and rebirth effect. Considering its long evolutionary history, scarcity of genetic variations and importance in wetland ecosystems, we appeal to take lawful measures to protect the wild lotus. For conservation purpose, special attention should be paid to the lotus at the middle reaches of the Songhua River Valley.

Inbreeding and Endangered Species Management: Is New Zealand Out of Step with the Rest of the World?

There is growing evidence that inbreeding can negatively affect small, isolated populations. This contrasts with the perception in New Zealand, where it has been claimed that native birds are less affected by inbreeding depression than threatened species from continental regions. It has been argued that New Zealand's terrestrial birds have had a long history of small population size with frequent inbreeding and that this has 'purged" deleterious alleles. The rapid recovery of many tiny and inbred populations after introduced predators have been controlled, and without input from more genetically diverse populations, has further supported the view that inbreeding is not a problem. This has led to a general neglect of inbreeding as a factor in recovery programs for highly endangered species such as the Black Robin (Petroica traversi) and Kakapo (Strigops habroptilis). We examined the reasons for this situation and review the New Zealand evidence for genetic purging. Complete purging of the genetic load and elimination of inbreeding depression are unlikely to occur in natural populations, although partial purging may be more likely where small populations have become inbred over an extended period of time, such as on small isolated islands. Recent molecular data are consistent with the view that island endemics, including New Zealand's threatened birds, have low genetic variation and hence have possibly gone through longer periods of inbreeding than threatened species from continental regions. Nevertheless, results from recent field studies in New Zealand indicate that, despite the opportunity for purging, inbreeding depression is evident in many threatened species. Although inbreeding depression has not prevented some populations from recovering from severe bottlenecks, the long-term consequences of inbreeding and small population size--the loss of genetic variation--are potentially much more insidious. The degrees to which genetic factors reduce population viability generally remain unquantified in New Zealand. Although minimizing ecological risks (e.g., preventing reinvasion of islands by mammalian predators) will continue to receive high priority in New Zealand because of their much larger impacts, we advocate that genetic considerations be better integrated into recovery plans.

Accelerating rotation of high-resolution images

Real-time image rotation is an essential operation in many application areas such as image processing, computer graphics and pattern recognition. Existing architectures that rely on CORDIC computations for trigonometric operations cause a severe bottleneck in high-throughput applications, especially where high-resolution images are involved. A novel hierarchical method that exploits the symmetrical characteristics of the image to accelerate the rotation of high-resolution images is presented. Investigations based on a 512×512 image show that the proposed method yields a speedup of ∼20× for a mere 3% increase in area cost when compared with existing techniques. Moreover, the effect of hierarchy on the computational efficiency has been evaluated to provide for area–time flexibility. The proposed technique is highly scalable and significant performance gains are evident for very high-resolution images.

Landscape attributes and life history variability shape genetic structure of trout populations in a stream network

Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective.

Reproductive Strategies Explain Genetic Diversity in Atlantic Salmon, Salmo salar

We investigated the relationship between conservation status and genetic variability in European and North American Atlantic salmon, Salmo salar, populations, many of which have suffered severe bottlenecks. A negative north--south cline exists for the status of population conservation in this species. A literature review of genetic variability and demographic parameters of wild Atlantic salmon populations resulted in no statistical associations between population conservation status and genetic variation at enzyme or VNTR loci. We found however, a negative relationship between male parr maturation rates and geographical latitude for both American and European populations. The increase in effective population size due to participation by mature male parr and the increased proportions of these males in smaller (southern) populations could explain the lack of expected relationship between genetic variation and conservation status.

Mitochondrial phylogeography of the Eurasian beaverCastor fiberL.

Nucleotide variation in an approximately 490 bp fragment of the mitochondrial DNA control region (mtDNA CR) was used to describe the genetic variation and phylogeographical pattern in the Eurasian beaver (Castor fiber) over its entire range. The sampling effort was focused on the relict populations that survived a drastic population bottleneck, caused by overhunting, at the end of the 19th century. A total of 152 individuals grouped into eight populations representing all currently recognized subspecies were studied. Sixteen haplotypes were detected, none of them shared among populations. Intrapopulation sequence variation was very low, most likely a result of the severe bottleneck. Extreme genetic structure could result from human-mediated extinction of intermediate populations, but it could also be an effect of prior substantial structuring of the beaver populations with watersheds of major Eurasian rivers acting as barriers to gene flow. Phylogenetic analysis revealed the presence of two mtDNA lineages: eastern (Poland, Lithuania, Russia and Mongolia) and western (Germany, Norway and France), the former comprising more divergent haplotypes. The low level of sequence divergence of the entire cytochrome b gene among six individuals representing six subspecies suggests differentiation during the last glacial period and existence of multiple glacial refugia. At least two evolutionary significant units (ESU) can be identified, the western and the eastern haplogroup. The individual relict populations should be regarded as management units, the eastern subspecies possibly also as ESUs. Guidelines for future translocations and reintroductions are proposed.

NATIVE OR NATURALIZED? VALIDATING ALPINE CHAMOIS HABITAT MODELS WITH ARCHAEOZOOLOGICAL DATA

Conservation of mammal species often requires the application of predictive habitat models. While empirical models can indicate the potential suitability and distribution of recent habitat, they may fail to depict native habitat and distribution. Therefore, we advocate validating such models with archaeozoological data.To demonstrate the power of archaeozoological data in investigating native distribution patterns, we use the alpine chamois (Rupicapra rupicapra) as a model species. After experiencing a severe historical population bottleneck due to overexploitation, chamois populations recovered markedly during the last century. Fostered by humans and having profited from translocations, this alpine ungulate greatly expanded its range and began to invade forested areas both within and outside the Alps, where damage to vegetation was soon obvious. Consequently, a controversy arose concerning the natural distribution and habitat of chamois. To study the native habitat and distribution of alpine chamois in Switzerland, we focus on the Late Mesolithic and Neolithic period (6000–2200 BC). This period best suits our purpose because pristine forests then dominated the landscape and human influence was as yet minimal. We describe two opposing habitat models: the alpine model assumes that chamois had survived only in alpine areas, whereas the forest model assumes that they also roamed in steep, entirely forested areas. We validate these models with archaeozoological data. Because the probability of chamois bone occurrence in prehistoric settlements is expected to decrease with increasing distance from chamois habitat, the models differ in their geographical predictions of chamois bone records. Applying logistic regression models, only settlement proximity to chamois forest habitat explains recoveries of fossil chamois bones. The resulting function of catchment distances (i.e., the likelihood of hunting chamois depending on the distance between a settlement and the nearest chamois habitat) matches the spatial behavior of extant hunters within pristine forests.We conclude that Holocene chamois range in Switzerland naturally included steep and entirely forested regions, like the Jura Mountains. The recent invasion of these areas by chamois thus constitutes repatriation of native habitat. Accordingly, we propose a shift in perspective toward landscape integration of chamois.

Age, phylogeography and population structure of the microendemic banded spring snail,Mexipyrgus churinceanus

Recent theoretical and empirical studies of phylogeography and population structure indicate that many processes influence intraspecific evolutionary history. The present study represents the first examination of various forces influencing the spatial and temporal patterns of sequence variation in the freshwater Mexican banded spring snail, Mexipyrgus churinceanus. This snail occurs in one of the most critically endangered centres of freshwater endemism, the desert ecosystem of Cuatro Ciénegas. From cytochrome b mtDNA sequence variation, there is strong evidence of long-term isolation of three regions, suggesting that these regions represent evolutionarily distinct lineages. Molecular clock estimates of clade age indicate a time to most recent common ancestor of approximately 2.5 million years ago (Ma). The three regions differ considerably in the historical and demographic forces affecting population structure. The western populations have extremely low mtDNA diversity consistent with a severe bottleneck dating to 50,000 years before present (bp). The nearby Rio Mesquites drainage is characterized by fragmentation events, restricted gene flow with isolation by distance, and higher levels of mtDNA polymorphism. These patterns are consistent with the long-term stability of this drainage along with habitat heterogeneity and brooding contributing to population isolation and restricted gene flow. Southeastern populations show evidence of range expansion and a strong influence of genetic drift. Migration rates between drainages indicate very little gene flow between drainages except for asymmetric migration from the Rio Mesquites into both western and southeastern drainages.

Development of a novel ampholyte buffer for isoelectric focusing: electric charge-separation of protein samples for X-ray crystallography using free-flow isoelectric focusing

The purification of biological macromolecules has remained a severe bottleneck in three-dimensional structure determination in the field of protein crystallography. By the use of the Free Flow Electrophoresis (ProTeam FFE; TECAN Group Ltd) apparatus, target protein samples can be purified in a high yield, while a preparative separation is performed in solution without using solid matrices such as polyacrylamide gel. A novel ampholyte buffer suitable for crystallization in the use of the ProTeam FFE apparatus has been developed. This buffer is able to generate pH gradients owing to the use of low-molecular-weight electrolytes. The effect of the flow rate on the pH gradient using the novel ampholyte buffer has been elucidated. When the flow rate was lowered to 78 ml h(-1), the pH gradient in the electrophoretic chambers was generated in an almost linear fashion.

Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae)

Red pine (Pinus resinosa Ait.) is an ecologically and economically important forest tree species of northeastern North America and is considered one of the most genetically depauperate conifer species in the region. We have isolated and characterized 13 nuclear microsatellite loci by screening a partial genomic library with di-, tri-, and tetranucleotide repeat oligonucleotide probes. In an analysis of over 500 individuals representing 17 red pine populations from Manitoba through Newfoundland, five polymorphic microsatellite loci with an average of nine alleles per locus were identified. The mean expected and observed heterozygosity values were 0.508 and 0.185, respectively. Significant departures from Hardy-Weinberg equilibrium with excess homozygosity indicating high levels of inbreeding were evident in all populations studied. The population differentiation was high with 28-35% of genetic variation partitioned among populations. The genetic distance analysis showed that three northeastern (two Newfoundland and one New Brunswick) populations are genetically distinct from the remaining populations. The coalescence-based analysis suggests that "northeastern" and "main" populations likely became isolated during the most recent Pleistocene glacial period, and severe population bottlenecks may have led to the evolution of a highly selfing mating system in red pine.