High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

Funding was provided by the University of Ferrara, Italy. CvO was funded by the Earth and Life Systems Alliance (ELSA), Norwich Research Park, UKBackground: Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species' ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity. Results: With large variance in reproductive success (V-k >= 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima's D test) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR. Conclusions: Our results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck.Publisher PDFPeer reviewe

Computer simulations: Tools for population and evolutionary genetics

Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes whose interactions cannot be analytically predicted. Simulations have traditionally been used in population genetics by a fairly small community with programming expertise, but the recent availability of dozens of sophisticated, customizable software packages for simulation now makes simulation an accessible option for researchers in many fields. The in silico genetic data produced by simulations, along with greater availability of population-genomics data, are transforming genetic epidemiology, anthropology, evolutionary and population genetics and conservation. In this Review of the state-of-the-art of simulation software, we identify applications of simulations, evaluate simulator capabilities, provide a guide for their use and summarize future directions. © 2012 Macmillan Publishers Limited. All rights reserved

Zip file containing parameter files, analysis scripts, and example output files

This zip files contains 4 parameter files for running in Simcoal, 4 example data files in Arlequin format, 2 analysis scripts written in java, a readme file, and 2 example output files which contain final results in terms of power at M-ratio and heterozygote excess test. These files, and how to run analysis, are described in the readme text file, which can be opened in notepad

Bringing genetic diversity to the forefront of conservation policy and management

In this essay we explore questions on how to increase the visibility and utility of genetic information for biodiversity managers and policy makers. This is discussed in the light of Aichi CBD Target 13, which for the first time impels signatories to minimise genetic erosion and safe-guard genetic diversity. Drawing on qualitative results from a questionnaire sent to European conservation pro-fessionals by the ConGRESS Framework 7 Support Action(www.congressgenetics.eu), we summarise our preliminary findings on the attitudes and experiences of European conservation professionals in using genetics. We then dis- cuss the implications of these findings for academics involved in conservation genetics and suggest that a much closer partnership between academic conservation geneticists and conservation practitioners is necessary if the full potential of genetic tools in conservation is to be realised.Peer reviewe

End-of-Life Care in High-Grade Glioma Patients. The Palliative and Supportive Perspective

High-grade gliomas (HGGs) are the most frequently diagnosed primary brain tumors. Even though it has been demonstrated that combined surgical therapy, chemotherapy, and radiotherapy improve survival, HGGs still harbor a very poor prognosis and limited overall survival. Differently from other types of primary neoplasm, HGG manifests also as a neurological disease. According to this, palliative care of HGG patients represents a peculiar challenge for healthcare providers and caregivers since it has to be directed to both general and neurological cancer symptoms. In this way, the end-of-life (EOL) phase of HGG patients appears to be like a journey through medical issues, progressive neurological deterioration, and psychological, social, and affective concerns. EOL is intended as the time prior to death when symptoms increase and antitumoral therapy is no longer effective. In this phase, palliative care is intended as an integrated support aimed to reduce the symptoms burden and improve the Quality Of Life (QOL). Palliative care is represented by medical, physical, psychological, spiritual, and social interventions which are primarily aimed to sustain patients’ functions during the disease time, while maintaining an acceptable quality of life and ensuring a dignified death. Since HGGs represent also a family concern, due to the profound emotional and relational issues that the progression of the disease poses, palliative care may also relieve the distress of the caregivers and increase the satisfaction of patients’ relatives. We present the results of a literature review addressed to enlighten and classify the best medical, psychological, rehabilitative, and social interventions that are addressed both to patients and to their caregivers, which are currently adopted as palliative care during the EOL phase of HGG patients in order to orientate the best medical practice in HGG management

Computer simulations: tools for population and evolutionary genetics

Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes whose interactions cannot be analytically predicted. Simulations have traditionally been used in population genetics by a fairly small community with programming expertise, but the recent availability of dozens of sophisticated, customizable software packages for simulation now makes simulation an accessible option for researchers in many fields. The in silico genetic data produced by simulations, along with greater availability of population-genomics data, are transforming genetic epidemiology, anthropology, evolutionary and population genetics and conservation. In this Review of the state-of-the-art of simulation software, we identify applications of simulations, evaluate simulator capabilities, provide a guide for their use and summarize future directions.Peer reviewe