The neutralist-selectionist debate and estimates of allozyme multilocus structure in conservation genetics of the primitive land races of Ethiopian barley.
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Biological Evolution↗
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Conserved genetic basis of a quantitative plumage trait involved in mate choice.
A key question in evolutionary genetics is whether shared genetic mechanisms underlie the independent evolution of similar phenotypes across phylogenetically divergent lineages. Here we show that in two classic examples of melanic plumage polymorphisms in birds, lesser snow geese (Anser c. caerulescens) and arctic skuas (Stercorarius parasiticus), melanism is perfectly associated with variation in the melanocortin-1 receptor (MC1R) gene. In both species, the degree of melanism correlates with the number of copies of variant MC1R alleles. Phylogenetic reconstructions of variant MC1R alleles in geese and skuas show that melanism is a derived trait that evolved in the Pleistocene.
Animals↗
matB, a common fimbrillin gene of Escherichia coli, expressed in a genetically conserved, virulent clonal group.
A novel fimbrial type in Escherichia coli was identified and characterized. The expression of the fimbria was associated with the O18acK1H7 clonal group of E. coli, which cause newborn meningitis and septicemia when grown at low temperature; hence, it was named the Mat (meningitis associated and temperature regulated) fimbria. The fimbriae were purified from a fimA::cat sfaA::Gm fliC::St derivative of the O18K1H7 isolate E. coli IHE 3034. The purified Mat fimbrillin had an apparent molecular mass of 18 kDa and did not serologically cross-react with the type 1 or S fimbria of the same strain. The matB gene encoding the major fimbrillin was cloned from the genomic DNA of the fimA::cat sfaA::Gm fliC::St derivative of IHE 3034. The predicted MatB sequence was of 195 amino acids, contained a signal sequence of 22 residues, and did not show significant homology to any of the previously characterized fimbrial proteins. The DNA sequence of matB was 97.8% identical to a region from nucleotides 17882 to 18469 in the 6- to 8-min region of the E. coli K-12 chromosome, reported to encode a hypothetical protein. The 7-kb DNA fragment containing matB of IHE 3034 was found by restriction mapping and partial DNA sequencing to be highly similar to the corresponding region in the K-12 chromosome. Trans complementation of the matB::cat mutation in the IHE 3034 chromosome showed that matB in combination with matA or matC restored surface expression of the Mat fimbria. A total of 27 isolates representing K-12 strains and the major pathogroups of E. coli were analyzed for the presence of a matB homolog as well as for expression of the Mat fimbria. A conserved matB homolog was found in 25 isolates; however, expression of the Mat fimbriae was detected only in the O18acK1H7 isolates. Expression of the Mat fimbria was temperature regulated, with no or a very small amount of fimbriae or intracellular MatB fimbrillin being detected in cells cultivated at 37(o)C. Reverse transcriptase PCR and complementation assays with mat genes controlled by the inducible trc promoter indicated that regulation of Mat fimbria expression involved both transcriptional and posttranscriptional events.
Amino Acid Sequence↗
Biochemical and genetic conservation of fission yeast Dsk1 and human SR protein-specific kinase 1.
Arginine/serine-rich (RS) domain-containing proteins and their phosphorylation by specific protein kinases constitute control circuits to regulate pre-mRNA splicing and coordinate splicing with transcription in mammalian cells. We present here the finding that similar SR networks exist in Schizosaccharomyces pombe. We previously showed that Dsk1 protein, originally described as a mitotic regulator, displays high activity in phosphorylating S. pombe Prp2 protein (spU2AF59), a homologue of human U2AF65. We now demonstrate that Dsk1 also phosphorylates two recently identified fission yeast proteins with RS repeats, Srp1 and Srp2, in vitro. The phosphorylated proteins bear the same phosphoepitope found in mammalian SR proteins. Consistent with its substrate specificity, Dsk1 forms kinase-competent complexes with those proteins. Furthermore, dsk1(+) gene determines the phenotype of prp2(+) overexpression, providing in vivo evidence that Prp2 is a target for Dsk1. The dsk1-null mutant strain became severely sick with the additional deletion of a related kinase gene. Significantly, human SR protein-specific kinase 1 (SRPK1) complements the growth defect of the double-deletion mutant. In conjunction with the resemblance of dsk1(+) and SRPK1 in sequence homology, biochemical properties, and overexpression phenotypes, the complementation result indicates that SRPK1 is a functional homologue of Dsk1. Collectively, our studies illustrate the conserved SR networks in S. pombe consisting of RS domain-containing proteins and SR protein-specific kinases and thus establish the importance of the networks in eucaryotic organisms.
Amino Acid Sequence↗
Conservation genetics.
Inbreeding depression, accumulation and loss of deleterious mutations, loss of genetic variation in small populations, genetic adaptation to captivity and its effect on reintroduction success, and outbreeding depression are reviewed. The impact of genetic factors in endangerment and extinction has been underestimated in some recent publications. Inbreeding depression in wildlife and in the field has been clearly established, while its impact has been greatly underestimated. The size of populations where genetic factors become important is higher than previously recognized, as Ne/N ratios average 0.11. Purging effects have been overestimated as a mechanism for eliminating deleterious alleles in small populations. The impact of loss of genetic variation in increasing the susceptibility of populations to environmental stochasticity and catastrophes has generally been ignored. Consequently, extinctions are often attributed to "nongenetic" factors when these may have interacted with genetic factors to cause extinction.
Adaptation, Biological↗
The use of AFLP markers in conservation genetics--a case study on Pulsatilla vernalis in the Polish lowlands.
Pulsatilla vernalis is a rare species in the Polish lowlands, strongly threatened by anthropogenic disturbance of its habitats. A grave decrease in its populations has been observed during the past 60-80 years (analogous populations in Eastern Austria and the Czech Republic are almost or completely extinct). An analysis of the genetic diversity of populations in the Polish lowlands was performed to estimate its level and distribution. The AFLP method was used for the study of seven populations. An analysis using five pairs of selective primers revealed 446 scorable fragments; 62.1% of them were polymorphic. The average gene diversity indices was 0.17 (the mean value for all the populations), ranging from 0.139 to 0.204. A weak relationship between diversity and population size was revealed. Most of the genetic diversity was contributed to by the within-population level (AMOVA) and only a weak geographical structure was shown by UPGMA clustering. Four populations formed population-specific clusters while three others (from one region) were intermixed. These preliminary results show a moderate genetic diversity of the studied populations, which was still rather high when compared with their size. This result, together with the low between-population differentiation in the region, suggests that these populations are the remnants of larger populations that, only a few decades ago, were much less isolated.
Genetic Markers↗
[MHC and its application in the population and conservation genetics].
The major histocompatibility complex (MHC),with the highest genetic polymorphism,is a cluster of genes involved in immune response regulation in the vertebrates.MHC can provide information such as population genetic diversity,evolutionary history and population dynamics,and population genetic structure etc. It can also be applied in the captive breeding programme for endangered vertebrate species.
English Abstract↗
Identification of conserved genetic functions in Bacillus by use of temperature-sensitive mutants.
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Bacillus subtilis↗
Genetics and conservation biology.
Conservation genetics encompasses genetic management of small populations, resolution of taxonomic uncertainties and management units, and the use of molecular genetic analyses in forensics and to understanding species' biology. The role of genetic factors in extinctions of wild populations has been controversial, but evidence now shows that they make important contributions to extinction risk. Inbreeding has been shown to cause extinctions of wild populations, computer projections indicate that inbreeding depression has important effects on extinction risk, and most threatened species show signs of genetic deterioration. Inappropriate management is likely to result if genetic factors are ignored in threatened species management.
Animals↗
Conservation of genetic information: a code for site-specific DNA recognition.
We present findings of genetic information conservation between the glucocorticoid response element (GRE) DNA and the cDNA encoding the glucocorticoid receptor (GR) DNA-binding domain (DBD). The regions of nucleotide sub-sequence similarity to the GRE in the GR DBD occur specifically at nucleotide sequences on the ends of exons 3,4, and 5 at their splice junction sites. These sequences encode the DNA recognition helix on exon 3, a beta-strand on exon 4, and a putative alpha-helix on exon 5, respectively. The nucleotide sequence of exon 5 that encodes the putative alpha-helix located on the carboxyl terminus of the GR DBD shares sequence similarity with the flanking nucleotide regions of the GRE. We generated a computer model of the GR DBD using atomic coordinates derived from nuclear magnetic resonance spectroscopy to which we attached the exon 5-encoded putative alpha-helix. We docked this GR DBD structure at the 39-base-pair nucleotide sequence containing the GRE binding site and flanking nucleotides, which contained conserved genetic information. We observed that amino acids of the DNA recognition helix, the beta-strand, and the putative alpha-helix are spatially aligned with trinucleotides identical to their cognate codons within the GRE and its flanking nucleotides.
Amino Acid Sequence↗
Estimating pairwise relatedness from dominant genetic markers.
Knowledge of the genetic relatedness between a pair of individuals is important in many research areas of quantitative genetics, conservation genetics, evolution and ecology. Many estimators have been developed to estimate such pairwise relatedness (r) using codominant markers, such as microsatellites and enzymes. In contrast, only two estimators are proposed to use dominant markers, such as random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs), in relatedness inference. They are both biased estimators, and their statistical properties and robustness to the sampling errors in allele frequency have not been investigated. In this short paper, I propose two new pairwise relatedness estimators for dominant markers, and compare them in precision, accuracy and robustness to sampling with the two previous estimators using simulations. It was found that the new estimator based on the least squares approach is unbiased when allele frequencies are known or estimated from a sample without correcting for sampling effects. It has, however, a low precision and as a result, an intermediate overall performance among the four estimators in terms of the mean squared deviation (MSD) of estimates from actual values of r. The new estimator based on a similarity index is slightly biased but has generally the lowest MSD among the four estimators compared, regardless of the number of loci, type of actual relationships, allele frequencies known or estimated from samples. Simulations also show that the confidence intervals estimated by bootstrapping are appropriate for different estimators provided that the number of loci used in the estimation is not small.
Computer Simulation↗
[Intraspecific genetic diversity: monitoring and principles of conservation].
Genetic differentiation of a species, estimated on average according to the aggregate of allozyme loci, corresponds to a selectively neutral process. Such evolution is traditionally regarded as Markov's chain, in which the genetic dynamics of a population cannot be predicted for more than one generation. According to the concept of population systems, however, intraspecific differentiation can be interpreted as a process with memory, which retains information about the genetic structure of the ancestral population. This memory is maintained due to the organizing effect of gene immigration whose intensity is the higher, the lower the effective size of the local population. The ratio between intra- and inter-population components of gene diversity is maintained at a stable (optimal) level. Consequently, it can be regarded as the basic "reference point" in genetic monitoring of subdivided populations that have evolved under anthropogenic pressure. Such influences, altering established systemic links, distort the balance between differentiation and integration of the species gene pool and lead to adverse effects. Depending on the predominance of the inter- or intra-population component of gene diversity, these influences may be equivalent to outbreeding with an increased segregational load or to inbreeding, respectively. In the first case, the genetic process is adaptive, and, provided the negative influence is terminated in due time, it is possible to restore the genetic structure and normalize reproduction of gene pools in populations. In the second case, the genetic process is maladaptive and leads to degradation of populations. If one knows principles of the systemic organization of a species, it is possible to develop an approach to solving the problem of conservation of biological diversity by organizing non-exhaustive wildlife management.
Adaptation, Biological↗
Genetic diversity and phylogeography of the Apennine yellow-bellied toad Bombina pachypus, with implications for conservation.
Genetic variation was investigated in 17 populations of the Italian endemic Apennine yellow-bellied toad using both mitochondrial (598 bp of the cytochrome b gene) and nuclear (21 allozyme loci) markers. Populations from central Calabria (southern Italy) showed the highest levels of intrapopulation genetic variation, whereas samples located north of this region were nearly lacking in variation. This appears to be a typical pattern of 'southern richness and northern purity', usually attributed to the prolonged population stability within southern refugia coupled with the loss of variation during postglacial northward expansion. However, the overall pattern of genetic variation observed has a strong geographical component, suggesting two Calabrian plains, Catanzaro and Crati-Sibari, as historical barriers to dispersal separating three population groups. These findings cannot be explained by the prolonged stability of southern populations alone, and suggest that the southern richness has been at least in part shaped by allopatric differentiation within the refugial range, followed by intermixing of previously differentiated lineages. From a conservation standpoint, Calabria is the major genetic diversity reservoir for this species, thus deserving particular conservation efforts. Furthermore, although the low intrapopulation genetic variation outside Calabria appears to be of clear historical origin, evidence of a current reduction of gene flow suggests that human disturbance has also played a part, particularly in the anthropogenic impacted Volturno river drainage basin.
Alleles↗
Characterization and conservation of genetic diversity in subdivided populations.
We review the available tools for analysing genetic diversity in conservation programmes of subdivided populations. Ways for establishing conservation priorities have been developed in the context of livestock populations, both from the classical population genetic analysis and from the more recent Weitzman's approach. We discuss different reasons to emphasize either within or between-population variation in conservation decisions and the methodology to establish some compromise. The comparison between neutral and quantitative variation is reviewed from both theoretical and empirical points of view, and the different procedures for the dynamic management of conserved subdivided populations are discussed.
Animals↗
Quantitative genetics in conservation biology.
Most of the major genetic concerns in conservation biology, including inbreeding depression, loss of evolutionary potential, genetic adaptation to captivity and outbreeding depression, involve quantitative genetics. Small population size leads to inbreeding and loss of genetic diversity and so increases extinction risk. Captive populations of endangered species are managed to maximize the retention of genetic diversity by minimizing kinship, with subsidiary efforts to minimize inbreeding. There is growing evidence that genetic adaptation to captivity is a major issue in the genetic management of captive populations of endangered species as it reduces reproductive fitness when captive populations are reintroduced into the wild. This problem is not currently addressed, but it can be alleviated by deliberately fragmenting captive populations, with occasional exchange of immigrants to avoid excessive inbreeding. The extent and importance of outbreeding depression is a matter of controversy. Currently, an extremely cautious approach is taken to mixing populations. However, this cannot continue if fragmented populations are to be adequately managed to minimize extinctions. Most genetic management recommendations for endangered species arise directly, or indirectly, from quantitative genetic considerations.
Animals↗
Embryo transfer for conserving valuable genetic material from swine herds with pseudorabies.
Embryo transfer was used to conserve genetic material from 2 swine herds seropositive for pseudorabies virus (PRV). Embryos (n = 805) were recovered from 38 PRV-seropositive Duroc sows in Iowa and, after 4 to 10 hours' culture and shipment to Illinois, were transferred to 34 recipients from a herd seronegative for PRV. All recipients remained seronegative for PRV, and 22 of the recipients farrowed 208 pigs (189 alive) that also were seronegative for PRV. There was no evidence of PRV in the embryo recovery medium or in the uterine and oviductal cells recovered with the embryos. Transfer of morulae resulted in higher (P less than 0.02) farrowing rates than did transfer of 4- to 8-cell embryos, but litter size was not affected.
Animals↗
[Genetic risks in plant ex situ conservation].
Conserving genetic diversity of rare and endangered species and their evolutionary potential is one of the long-term goals of ex-situ conservation. Some potential genetic risks in ex-situ conservation in botanical gardens are presented. The preserved species may lack genetic representativity because of poor sampling. Inappropriate plantations, inadequate records and unclear kinships jeopardize endangered species to genetic confusion, inbreeding depression or outbreeding depression. Artificial selection and habitat conversion also potentially result endangered plants in adapting to ex-situ conservation, which had been usually overlooked. All the genetic risks can decrease the success of reintroduction and recovery. Therefore, appropriate genetic management should be carried out in botanical gardens to decrease or avoid genetic risks in ex-situ conservation.
Adaptation, Biological↗
The importance of immune gene variability (MHC) in evolutionary ecology and conservation.
Genetic studies have typically inferred the effects of human impact by documenting patterns of genetic differentiation and levels of genetic diversity among potentially isolated populations using selective neutral markers such as mitochondrial control region sequences, microsatellites or single nucleotide polymorphism (SNPs). However, evolutionary relevant and adaptive processes within and between populations can only be reflected by coding genes. In vertebrates, growing evidence suggests that genetic diversity is particularly important at the level of the major histocompatibility complex (MHC). MHC variants influence many important biological traits, including immune recognition, susceptibility to infectious and autoimmune diseases, individual odours, mating preferences, kin recognition, cooperation and pregnancy outcome. These diverse functions and characteristics place genes of the MHC among the best candidates for studies of mechanisms and significance of molecular adaptation in vertebrates. MHC variability is believed to be maintained by pathogen-driven selection, mediated either through heterozygote advantage or frequency-dependent selection. Up to now, most of our knowledge has derived from studies in humans or from model organisms under experimental, laboratory conditions. Empirical support for selective mechanisms in free-ranging animal populations in their natural environment is rare. In this review, I first introduce general information about the structure and function of MHC genes, as well as current hypotheses and concepts concerning the role of selection in the maintenance of MHC polymorphism. The evolutionary forces acting on the genetic diversity in coding and non-coding markers are compared. Then, I summarise empirical support for the functional importance of MHC variability in parasite resistance with emphasis on the evidence derived from free-ranging animal populations investigated in their natural habitat. Finally, I discuss the importance of adaptive genetic variability with respect to human impact and conservation, and implications for future studies.
Journal Article↗