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PubMed2000

Conservation genetics of bush mango from central/west Africa: implications from random amplified polymorphic DNA analysis.

Genetic variation was assessed in the two bush mango species, Irvingia gabonensis and I. wombolu, valuable multipurpose fruit trees from central and west Africa that are currently undergoing domestication. A total of 130 individuals sampled from Cameroon, Nigeria and Gabon were analysed using 74 random amplified polymorphic DNAs (RAPDs). Significant genetic integrity was found in the two morphologically similar species (among-species analysis of molecular variance [AMOVA] variance component 25.8%, P < 0.001), with no evidence of hybridization, even between individuals from areas of sympatry where hybridization was considered probable. Results suggest that large-scale transplantation of either species into new habitats will probably not lead to genetic introgression from or into the other species. Therefore, subsequent cultivation of the two species should not be hindered by this consideration, although further studies on the potential for hybridization/introgression between these species would be prudent. Significant genetic differentiation of both species (among-countries within species, nested AMOVA variance component 9.8%, P < 0.001) was observed over the sampled regions, and genetic similarity of samples decreased significantly with increasing geographical distance, according to number of alleles in common (NAC) analysis. 'Hot spots' of genetic diversity were found clustered in southern Nigeria and southern Cameroon for I. wombolu, and in southern Nigeria, southern Cameroon and central Gabon for I. gabonensis. The possible reasons for this distribution of genetic variation are discussed, but it may reflect evolutionary history, as these populations occur in areas of postulated Pleistocene refugia. The application of these results to domestication programmes and, in the light of extensive deforestation in the region, conservation approaches, is discussed.

Africa, Central↗
PubMed1985

Molecular biology of the human and mouse MHC class III genes: phylogenetic conservation, genetics and regulation of expression.

The generation of complementary and genomic DNA clones for the human and mouse MHC class III genes has advanced the study of the organization, structure, genetics and expression of these loci. These clones have been useful in defining new polymorphic markers in each species and therefore permit a more complete genetic analysis of the complement cluster and the MHC as a whole. The coding sequences of the factor B and C4 genes are extensively conserved both within and between species, in contrast to the coding sequences of other MHC products. In human and mouse, the organization of the class III genes is similar with respect to order and position between the class II and class I regions of the MHC. However, these inter-species similarities in the organization and products of the class III genes does not extend to their regulation. In addition to complement gene expression being regulated differently between tissue sites within a species, expression is apparently regulated differently in analogous tissues between species. The considerable progress which has been made in the molecular analysis of C2, factor B and C4 using DNA clones forms the basis for the future study of the biology of the class III genes and the role of complement in inflammatory processes and in the immune system.

Animals↗
PubMed1999

Phylogeography and conservation genetics of the Iowa pleistocene snail.

The Iowa Pleistocene snail, Discus macclintocki, is an endangered species that survives only in relictual populations on algific (cold-air) talus slopes in northeast Iowa and northwest Illinois in the central region of the USA. These populations are believed to have been isolated since the temperatures began to warm at the end of the last glacial period around 16 500 years ago. DNA sequencing of the 16s rRNA gene of the mitochondria was used to determine the genetic relationship among 10 populations and the genetic diversity within these populations. Genetic diversity is extremely high within this species with 40 haplotypes spread across the 10 populations sampled within a 4000 km2 region. Phylogenetic analyses showed that haplotypes formed monophyletic groups by the watershed on which they were found, suggesting that watersheds were important historical avenues of gene flow. Genetic distances were strongly related to the geographical distance among all populations, but this relationship was dependent on the scale being considered.

Animals↗
PubMed2003

Phylogeography and conservation genetics of Eld's deer (Cervus eldi).

Eld's deer (Cervus eldi) is a highly endangered cervid, distributed historically throughout much of South Asia and Indochina. We analysed variation in the mitochondrial DNA (mtDNA) control region for representatives of all three Eld's deer subspecies to gain a better understanding of the genetic population structure and evolutionary history of this species. A phylogeny of mtDNA haplotypes indicates that the critically endangered and ecologically divergent C. eldi eldi is related more closely to C. e. thamin than to C. e. siamensis, a result that is consistent with biogeographic considerations. The results also suggest a strong degree of phylogeographic structure both between subspecies and among populations within subspecies, suggesting that dispersal of individuals between populations has been very limited historically. Haplotype diversity was relatively high for two of the three subspecies (thamin and siamensis), indicating that recent population declines have not yet substantially eroded genetic diversity. In contrast, we found no haplotype variation within C. eldi eldi or the Hainan Island population of C. eldi siamensis, two populations which are known to have suffered severe population bottlenecks. We also compared levels of haplotype and nucleotide diversity in an unmanaged captive population, a managed captive population and a relatively healthy wild population. Diversity indices were higher in the latter two, suggesting the efficacy of well-designed breeding programmes for maintaining genetic diversity in captivity. Based on significant genetic differentiation among Eld's deer subspecies, we recommend the continued management of this species in three distinct evolutionarily significant units (ESUs). Where possible, it may be advisable to translocate individuals between isolated populations within a subspecies to maintain levels of genetic variation in remaining Eld's deer populations.

Animal Population Groups↗
PubMed2001

Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae).

The jaguar (Panthera onca), the largest felid in the American Continent, is currently threatened by habitat loss, fragmentation and human persecution. We have investigated the genetic diversity, population structure and demographic history of jaguars across their geographical range by analysing 715 base pairs of the mitochondrial DNA (mtDNA) control region and 29 microsatellite loci in approximately 40 individuals sampled from Mexico to southern Brazil. Jaguars display low to moderate levels of mtDNA diversity and medium to high levels of microsatellite size variation, and show evidence of a recent demographic expansion. We estimate that extant jaguar mtDNA lineages arose 280 000-510 000 years ago (95% CI 137 000-830 000 years ago), a younger date than suggested by available fossil data. No strong geographical structure was observed, in contrast to previously proposed subspecific partitions. However, major geographical barriers such as the Amazon river and the Darien straits between northern South America and Central America appear to have restricted historical gene flow in this species, producing measurable genetic differentiation. Jaguars could be divided into four incompletely isolated phylogeographic groups, and further sampling may reveal a finer pattern of subdivision or isolation by distance on a regional level. Operational conservation units for this species can be defined on a biome or ecosystem scale, but should take into account the historical barriers to dispersal identified here. Conservation strategies for jaguars should aim to maintain high levels of gene flow over broad geographical areas, possibly through active management of disconnected populations on a regional scale.

Animals↗
PubMed1994

Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe.

Some small European populations of the brown bear (Ursus arctos) are threatened by the risk of extinction in the near future. The reinforcement of these populations with bears from other regions might provide a solution to their future survival. However, before any population transfer, the different conservation units must be identified. The phylogeographic approach has been advocated for this purpose. The different European populations were assayed for mitochondrial (mt) DNA polymorphism. A remarkable degree of concordance was found between the geographic distribution and the mtDNA haplotypes. Two clearly distinct lineages differing by more than 7% in mtDNA control region sequences were found and, furthermore, the western lineage appears to be organized into two clades which correspond to two different ancestral refugia. The potential conservation units can be deduced from these results, and a management policy can consequently be inferred. This study clearly demonstrates the relevance of the molecular phylogeographic approach to the identification of conservation units.

Animals↗
PubMed1996

Genetic conservation of Highlands J viruses.

We studied molecular evolution of the mosquito-borne alphavirus Highlands J (HJ) virus by sequencing PCR products generated from 19 strains isolated between 1952 and 1994. Sequences of 1200 nucleotides including portions of the E1 gene and the 3' untranslated region revealed a relatively slow evolutionary rate estimated at 0.9-1.6 x 10(-4) substitutions per nucleotide per year. Phylogenetic trees indicated that all HJ viruses descended from a common ancestor and suggested the presence of one dominant lineage in North America. However, two or more minor lineages probably circulated simultaneously for periods of years to a few decades. Strains isolated from a horse suffering encephalitis, and implicated in a recent turkey outbreak, were not phylogenetically distinct from strains isolated in other locations during the same time periods. Our findings are remarkably similar to those we obtained previously for another North American alphavirus, eastern equine encephalomyelitis virus, with which Highlands J shares primary mosquito and avian hosts, geographical distribution, and ecology. These results support the hypotheses that the duration of the transmission season affects arboviral evolutionary rates and vertebrate host mobility influences genetic diversity.

Alphavirus↗
PubMed2001

Conserved genetic findings in metastatic bladder cancer: a possible utility of allelic loss of chromosomes 9p21 and 17p13 in diagnosis.

CONTEXT: Molecular analysis of microsatellite alterations of biologically distinct tumor cell subpopulations from the same patient may aid in the determination of tumor origin and further our understanding of the genetic basis of cancer progression. DESIGN: The authors examined the pattern of allelic loss with polymorphic microsatellite markers on chromosome 9p21 (D9S161, D9S171, IFNA), regions of putative tumor suppressor gene p16, and on chromosome 17p13 (TP53), the p53 locus, in matched primary and metastatic bladder cancers from 9 patients. All patients underwent cystectomy for bladder cancer and had regional lymph node metastases at the time of surgery. Genomic DNA was prepared from primary cancers and matched synchronous lymph node metastases using a microdissection method. RESULTS: The overall frequency of allelic loss was 78% in primary cancer and 89% in paired metastatic cancer. The frequency of allelic loss in the primary cancer was 86% with D9S161, 67% with D9S171, 71% with IFNA, and 80% with TP53. The frequency of allelic loss in matched metastatic cancer was 100% with D9S161, 62% with D9S171, 71% with IFNA, and 80% with TP53. An identical pattern of allelic imbalance (allelic loss or retention) at multiple DNA loci was observed in matched primary and metastatic carcinoma in 8 (88%) cases. One case showed allelic loss in the metastasis, but not in the primary cancer. CONCLUSIONS: The pattern of allelic loss at chromosome 9p21 (p16) and 17p13 (p53) was generally maintained during cancer progression to metastasis, and identical allelic loss in primary cancer was conserved in paired metastatic carcinoma. These data suggest that these genetic changes may be useful in establishing a diagnosis and determining tumor origins in difficult cases.

Aged↗
PubMed1992

Evolution of influenza B/Victoria/2/87-like viruses: occurrence of a genetically conserved virus under conditions of low epidemic activity.

Nucleotide sequence analysis of the gene region coding for the HA1 domain of the influenza B virus haemagglutinin was performed on seven field strains isolated during the 1989 to 1990 season and two field strains isolated in 1985 and 1988 in Finland. All isolates were antigenically and genetically related to B/Victoria/2/87 virus and distinct from B/Yamagata/16/88 virus. The three strains isolated at the beginning of the 1989 1990 season in Turku were almost identical to an American variant (B/Texas/37/88-B/Ohio/10/88) of the previous season, whereas the four strains isolated later in the 1989 to 1990 season in Helsinki formed a new group of heterogeneous viruses. The phylogenetic tree compiled suggests that the two branches had evolved from a common origin, probably in 1987.

Amino Acid Sequence↗
PubMed2000

Genetic conservation of the immunophilin-binding domains of human calcineurin A1 and A2.

Calcineurin a calmodulin-dependent phosphatase plays a critical role in calcium-dependent activation of T-lymphocytes and is the major target for the inhibitory actions of the immunosuppressive drugs Tacrolimus (FK506) and Cyclosporin A (CsA). Calcineurin is a dimeric protein consisting of distinct A (catalytic) and B (regulatory) subunits. In humans two separate genes, CNA1 and CNA2, encode the calcineurin A (CNA) subunit. The region of CNA that interacts with Calcineurin B, calmodulin, and immunosuppressive drugs bound to their receptors--the immunophilins--has been identified to amino acids 281-414 (Greengard P, Allen PB, Nairin AC. Beyond the dopamine receptor: the DARPP-32/protein phosphatase-1 cascade. Neuron 1999;23:435). Our working hypothesis was that the differences in patient response to calcineurin inhibitors could be a consequence of inherited variations within their CNA genes. Single-strand conformational polymorphism (SSCP) analysis of cDNAs derived from the coding region for amino acids 281-414 of CNA1 and CNA2 in 32 healthy Caucasians did not detect polymorphic variations within these genes. These results suggest that this region is highly conserved and cannot account for individual variation in response of patients to FK506 and CsA treatment.

Binding Sites↗
PubMed2004

Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex.

The red-legged frog, Rana aurora, has been recognized as both a single, polytypic species and as two distinct species since its original description 150 years ago. It is currently recognized as one species with two geographically contiguous subspecies, aurora and draytonii; the latter is protected under the US Endangered Species Act. We present the results of a survey of 50 populations of red-legged frogs from across their range plus four outgroup species for variation in a phylogenetically informative, approximately 400 base pairs (bp) fragment of the mitochondrial cytochrome b gene. Our mtDNA analysis points to several major results. (1) In accord with several other lines of independent evidence, aurora and draytonii are each diagnosably distinct, evolutionary lineages; the mtDNA data indicate that they do not constitute a monophyletic group, but rather that aurora and R. cascadae from the Pacific northwest are sister taxa; (2) the range of the draytonii mtDNA clade extends about 100 km further north in coastal California than was previously suspected, and corresponds closely with the range limits or phylogeographical breaks of several codistributed taxa; (3) a narrow zone of overlap exists in southern Mendocino County between aurora and draytonii haplotypes, rather than a broad intergradation zone; and (4) the critically endangered population of draytonii in Riverside County, CA forms a distinct clade with frogs from Baja California, Mexico. The currently available evidence favours recognition of aurora and draytonii as separate species with a narrow zone of overlap in northern California.

Animals↗
PubMed2004

Conservation genetics and demographic history of the endangered Cape Fear shiner (Notropis mekistocholas).

We examined allelic variation at 22 nuclear-encoded markers (21 microsatellites and one anonymous locus) and mitochondrial (mt)DNA in two geographical samples of the endangered cyprinid fish Notropis mekistocholas (Cape Fear shiner). Genetic diversity was relatively high in comparison to other endangered vertebrates, and there was no evidence of small population effects despite the low abundance reported for the species. Significant heterogeneity (following Bonferroni correction) in allele distribution at three microsatellites and in haplotype distribution in mtDNA was detected between the two localities. This heterogeneity may be due to reduced gene flow caused by a dam built in the early 1900 s. Bayesian coalescent analysis of microsatellite variation indicated that effective population size of Cape Fear shiners has declined in recent times (11-25 435 years ago, with highest posterior probabilities between 126 and 2007 years ago) by one-two orders of magnitude, consistent with the observed decline in abundance of the species. A decline in effective size was not indicated by analysis of mtDNA, where sequence polymorphism appeared to carry the signature of an older expansion phase that dated to the Pleistocene ( approximately 12 700 > 1 million years ago). Cape Fear shiners thus appear to have undergone an expansion phase following a glacial cycle but to have declined significantly in more recent times. These results suggest that rapidly evolving markers such as microsatellites may constitute a suitable tool when inferring recent demographic dynamics of populations.

Animals↗
PubMed2005

Phylogeography and conservation genetics of Hygrophila pogonocalyx (Acanthaceae) based on atpB-rbcL noncoding spacer cpDNA.

Genetic variation in the atpB-rbcL intergenic spacer region of chloroplast DNA (cpDNA) was investigated in Hygrophila pogonocalyx Hayata (Acanthaceae), an endangered and endemic species in Taiwan. In this aquatic species, seed dispersal from capsules via elasticity is constrained by gravity and is thereby confined within populations, resulting in limited gene flow between populations. In this study, a total of 849 bp of the cpDNA atpB-rbcL spacer were sequenced from eight populations of H. pogonocalyx. Nucleotide diversity in the cpDNA is low (theta = 0.00343+/-0.00041). The distribution of genetic variation among populations agrees with an "isolation-by-distance" model. Two geographically correlated groups, the western and eastern regions, were identified in a neighbor-joining tree and a minimum-spanning network. Phylogeographical analyses based on the cpDNA network suggest that the present-day differentiation between western and eastern groups of H. pogonocalyx resulted from past fragmentation. The differentiation between eastern and western populations may be ascribed to isolation since the formation of the Central Mountain Range about 5 million years ago, which is consistent with the rate estimates based on a molecular clock of cpDNA.

Acanthaceae↗
PubMed2003

Positive assortative mating with selection restrictions on group coancestry enhances gain while conserving genetic diversity in long-term forest tree breeding.

Selection and mating principles in a closed breeding population (BP) were studied by computer simulation. The BP was advanced, either by random assortment of mates (RAM), or by positive assortative mating (PAM). Selection was done with high precision using clonal testing. Selection considered both genetic gain and gene diversity by "group-merit selection", i.e. selection for breeding value weighted by group coancestry of the selected individuals. A range of weights on group coancestry was applied during selection to vary parent contributions and thereby adjust the balance between gain and diversity. This resulted in a series of scenarios with low to high effective population sizes measured by status effective number. Production populations (PP) were selected only for gain, as a subset of the BP. PAM improved gain in the PP substantially, by increasing the additive variance (i.e. the gain potential) of the BP. This effect was more pronounced under restricted selection when parent contributions to the next generation were more balanced with within-family selection as the extreme, i.e. when a higher status effective number was maintained in the BP. In that case, the additional gain over the BP mean for the clone PP and seed PPs was 32 and 84% higher, respectively, for PAM than for RAM in generation 5. PAM did not reduce gene diversity of the BP but increased inbreeding, and in that way caused a departure from Hardy-Weinberg equilibrium. The effect of inbreeding was eliminated by recombination during the production of seed orchard progeny. Also, for a given level of inbreeding in the seed orchard progeny or in a mixture of genotypes selected for clonal deployment, gain was higher for PAM than for RAM. After including inbreeding depression in the simulation, inbreeding was counteracted by selection, and the enhancement of PAM on production population gain was slightly reduced. In the presence of inbreeding depression the greatest PP gain was achieved at still higher levels of status effective number, i.e. when more gene diversity was conserved in the BP. Thus, the combination of precise selection and PAM resulted in close to maximal short-term PP gain, while conserving maximal gene diversity in the BP.

Computer Simulation↗
PubMed1993

Genetic conservation of hlyA determinants and serological conservation of HlyA: basis for developing a broadly cross-reactive subunit Escherichia coli alpha-hemolysin vaccine.

The HlyA determinant among Escherichia coli isolates from patients with symptomatic urinary tract infection was compared in this report with a prototype HlyA encoded by pSF4000 by DNA-DNA hybridization tests with 20-base synthetic oligonucleotides and monoclonal antibody binding and neutralization assays. Hybridization results demonstrated that 349 (98%) of 357 definitive reactions among 54 hemolytic strains shared homology with seven DNA probes spanning many HlyA regions corresponding to residues (R) 41 to 47, 55 to 61, 248 to 254, 306 to 312, 336 to 343, 402 to 408, and 929 to 935. Genetic divergence was identified by lack of hybridization signals among 17 to 76% of the hemolytic strains within the distal portion of a predicted hydrophobic region corresponding to R491 to 319 and within a predicted hydrophilic region corresponding to R491 to 497 and R532 to 538. Serological studies demonstrated that 26 (81%) culture supernatants of 32 hemolytic strains were bound by all 12 monoclonal anti-HlyA antibodies. Among five of six remaining strains, the culture supernatants were bound by 3 to 11 monoclonal antibody preparations. There was only one hemolytic culture supernatant that failed to be bound by any monoclonal antibody, although the strain hybridized with nine hemolysin DNA probes. In addition, hemolytic activity of all 24 different culture supernatants tested was reduced by at least twofold by one monoclonal antibody specific for R2-161. These data extend and support previous views that the HlyA determinant is conserved among E. coli strains and suggest that a broadly cross-reactive HlyA subunit vaccine can be developed.

Amino Acid Sequence↗
PubMed1994

Serotype G6 human rotavirus sharing a conserved genetic constellation with natural reassortants between members of the bovine and AU-1 genogroups.

Serotype G6 human rotavirus PA151 was examined by RNA-RNA hybridization in comparison with another G6 strain PA169 and two naturally-occurring G3 reassortants PCP5 and MZ58. PA151 possessed three gene segments that formed hybrids with AU-1 and seven gene segments that formed hybrids with bovine rotavirus NCDV. PA151 also possessed eight, 10 and 10 gene segments that formed hybrids with genomic RNAs from PA169, PCP5, and MZ58, respectively. Thus, PA151 was an intergenogroup reassortant formed in nature between members of the bovine and AU-1 genogroups and it shared a genome constellation with PA169, PCP5, and MZ58. These results suggest that naturally-occurring intergenogroup reassortants possessing such a genome constellation were perpetuated in human populations.

Animals↗
PubMed2004

The zebrafish onecut gene hnf-6 functions in an evolutionarily conserved genetic pathway that regulates vertebrate biliary development.

Targeted disruption of the onecut transcription factor, hnf-6, alters mammalian biliary system development. We have identified a related zebrafish cDNA expressed in the developing liver that is a functional ortholog of mammalian hnf-6. Antisense-mediated knockdown of zebrafish hnf-6 perturbs development of the intrahepatic biliary system. Knockdown of zebrafish hnf-6 alters expression of vhnf1 and the zebrafish orthologs of other mammalian genes regulated by hnf-6. Coinjection of mRNA encoding zebrafish vhnf1 rescues the biliary phenotype of hnf-6 morphants. These experiments strongly suggest that hnf-6 and vhnf1 function within an evolutionarily conserved pathway that regulates biliary development. Forced expression of either hnf-6 or vhnf1 also produces biliary phenotypes. Altered bile duct development in both loss- and gain-of-function experiments suggests that zebrafish biliary cells are sensitive to the dosage of hnf-6-mediated gene transcription.

Amino Acid Sequence↗
PubMed1995

Conservation genetics of the European brown bear--a study using excremental PCR of nuclear and mitochondrial sequences.

In the Brenta area of northern Italy, a brown bear Ursus arctos population is rapidly going extinct. Restocking of the population is planned. In order to study the genetics of this highly vulnerable population with a minimum of stress to the animals we have developed a PCR-based method that allows the study of mitochondrial and nuclear gene sequences from droppings collected in the field. This method is generally applicable to animals in the wild. Using excremental as well as hair samples, we show that the Brenta population is monomorphic for one mitochondrial lineage and that female as well as male bears exist in the area. In addition, 70 samples from other parts of Europe were studied. As others have previously reported, the mitochondrial gene pool of European bears is divided into two major clades, one with a western and the other with an eastern distribution. Whereas populations generally belong to either one or the other mitochondrial clade, the Romanian population contains both clades. The bears in the Brenta belong to the western clade. The implications for the management of brown bears in the Brenta and elsewhere in Europe are discussed.

Animals↗