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PubMed2006

Paucity of class I MHC gene heterogeneity between individuals in the endangered Hawaiian monk seal population.

The Hawaiian monk seal population has experienced precipitous declines in the last 50 years. In this study, we provide evidence that individuals from remaining endangered population exhibit alarming uniformity in class I major histocompatibility (MHC) genes. The peripheral blood leukocyte-derived mRNA of six captive animals rescued from a stranding incident on the French frigate shoals in the Hawaiian archipelago was used to characterize genes in the monk seal class I MHC gene family, from which techniques for genotyping the broader population were designed using degenerate primers designed for the three major established human MHC class I loci (HLA-A, HLA-B, and HLA-C), and by sequencing multiple clones, six unique full-length classical MHC class I gene transcripts were identified among the six animals, three of which were only found in single individuals. Since The low degree of sequence variation between these transcripts and the similarity of genotype between individuals provided preliminary evidence for low class I MHC variability in the population. The sequence information from the class I transcripts from these six animals was used to design several primer sets for examining the extent of MHC variability in the remaining population using a combination of polymerase chain reaction and denaturing gradient gel electrophoresis (DGGE). Several DGGE assays, each one amplifying subtly different class I MHC gene combinations, were designed to compare exons encoding the highly polymorphic domains of the putative peptide-binding region of MHC class I. In combination, these assays failed to show interindividual variability at any of the class I MHC gene loci examined in either the six captive seals or in 80 free-ranging animals ( approximately 6.7% of the estimated population) representing all six major subpopulations of Hawaiian monk seal.

Base Sequence↗
PubMed2001

Class I MHC polymorphism and evolution in endangered California Chinook and other Pacific salmon.

Twelve MHC class I exon 2 sequences were uncovered in a sample from the endangered Sacramento River winter-run Chinook salmon in the central valley of California. Phylogenetic analysis of the 12 sequences indicates that the alleles descend from two of six major allelic lineages found among four Pacific salmon species. Nine of the 12 alleles belong to an allelic lineage that began diversifying 8 million years ago, just prior to the estimated time of Chinook speciation. The most recent common ancestor of all 12 winter-run alleles is estimated to be 15 million years ago, approximately 5 million years before the radiation of the Pacific salmon species. The average nonsynonymous distance among the peptide binding-region codons of exon 2 for the 12 alleles is significantly higher than the average synonymous distance in these codons. We estimate the symmetrical overdominant selection coefficient against homozygotes for this exon to be 0.038. Thus, strong positive and balancing selection has maintained functional diversity in the peptide-binding region of the exon over millions of years and this variation has not yet been substantially eliminated by increased genetic drift due to the recent dramatic decline in abundance of this Chinook salmon population.

Evolution, Molecular↗
PubMed2006

Managing an endangered Asian bovid in an Australian National Park: the role and limitations of ecological-economic models in decision-making.

Should north Australia's extensive populations of feral animals be eradicated for conservation, or exploited as a rare opportunity for Indigenous enterprise in remote regions? We examine options for a herd of banteng, a cattle species endangered in its native Asian range but abundant in Garig Gunak Barlu National Park, an Aboriginal land managed jointly by traditional owners and a conservation agency in the Northern Territory of Australia. We reflect on the paradoxes that arise when trying to deal effectively with such complex and contested issues in natural resource management using decision-support tools (ecological-economic models), by identifying the trade-offs inherent in protecting values whilst also providing incomes for Indigenous landowners.

Animals↗
PubMed2000

A Crosswalk from the Endangered Species Act to the HCP Handbook and Real HCPs.

The U.S. Departments of Interior and Commerce published the HCP handbook in 1996 to guide the issuance of incidental take permits (ITPs). The HCP handbook lists six guidelines and provides many others throughout the text. However, the guidelines sometimes contradict the intent of the Endangered Species Act (ESA), and some are vague due to their use of improperly defined terms, such as ecosystem, region(al), net benefits, and habitat types. A proposed addendum provides little improvement to the HCP handbook. The guidelines in the HCP handbook could be prepared to better match those that scientists would expect from the language of the ESA. Three HCPs met only 3-10% of the 39 guidelines I would expect based on the ESA, and they met only 7-20% of the 30 guidelines in the HCP handbook. Based on a recent legal decision on the Alabama Beach Mouse HCP, ITP applicants are expected to follow the guidelines in the HCP handbook. The three HCPs I reviewed are vulnerable to similar legal decisions. However, many of the guidelines in the HCP handbook are inconsistent with the ESA. Therefore, I recommend that the HCP handbook be revised so that it is consistent with the ESA and with academic standards in the use of scientific methods. The guidelines need to be more explicit to be operationally consistent. Such a revision would provide ITP applicants and all the stakeholders with much more certainty in the outcome of the process. In lieu of a revised HCP handbook, I recommend that ITP applicants prepare their HCPs using the standards presented in Smallwood and others (Environmental Management, 1999, 24:421-435), thereby giving their HCPs a strong scientific foundation.

Journal Article↗
PubMed2001

Decline in endangered species as an indication of anthropic pressures: the case of European mink Mustela lutreola Western population.

Populations of threatened species, especially predators at the top of the food chain, may be affected by anthropic pressures. The endangered western population of European mink Mustela lutreola has shown a large decline over 50% of its natural range. M. lutreola disappeared from northwestern France between 1984 and 1997, and the decline was associated with an increase in mustelid trapping, changes in watercourse quality, and habitat modifications due to agricultural practices. The pattern of decline showed a fragmentation restricting the minks into very small areas. Trapping was the first known cause of mortality. Although feral American mink Mustela vison may compete with autochthonous carnivores, M. lutreola had disappeared from streams before the introduction of the American species, suggesting that competitive interactions were not responsible. Furthermore, American mink has never been found or has remained rare in 62.4% of the area from which M. lutreola has disappeared. During the past 25 years, permanent grassland surfaces were reduced by 40%, whereas fodder culture increased by 470%, causing considerable habitat changes. Furthermore, 55.7% of water courses were classified as being of bad quality or polluted. Therefore, our data suggests that a conjunction of intensive trapping, alterations in water quality and habitat modification was critical for the European mink's decline. Although there are difficulties in ascribing specific cause to distribution changes in a top predator, this decline can be regarded as an indication for anthropic pressures on natural habitats.

Agriculture↗
PubMed2006

Rapid plant regeneration and analysis of genetic fidelity of in vitro derived plants of Chlorophytum arundinaceum Baker--an endangered medicinal herb.

An efficient in vitro multiplication system via multiple shoot bud induction and regeneration has been developed in Chlorophytum arundinaceum using shoot crown explants. Optimum regeneration frequency (87%) and desirable organogenetic response in the form of de novo organized multiple shoot buds without an intervening callus phase was obtained on Murashige and Skoog's (MS) minimal organics medium containing 3% sucrose (w/v) supplemented with 4 x 10(-6) M Kn and 2 x 10(-6) MIBA. Axenic secondary explants with multiple shoot buds on subculturing elicited best response with 1 x 10(-5) M Kinetin (Kn) and 5 x 10(-6) M indole-3-butyric acid (IBA) giving rise to an average of 18.74 shoots per culture with mean shoot length of 7.6 cm +/- 1.73. Varying molar ratios of either Kn/IBA or Kn/NAA revealed statistically significant differences in the regeneration frequencies among the phytohormone treatments. It was observed that the shoot bud differentiation and regeneration was influenced by the molar ratios of cytokinins/auxin rather than their relative concentrations. Healthy regenerated shoots were rooted in half strength MS basal medium containing 3% sucrose (w/v) supplemented with 5 x 10(-6) M IBA. Following simple hardening procedures, rooted plantlets, were transferred to soil-sand (1:1; v/v) with more than 90% success. Genetic fidelity was assessed using random amplified polymorphic DNA (RAPD), karyotype analysis and meiotic behaviour of in vitro and in vivo plants. Five arbitrary decamers displayed same banding profile within all the micropropagated plants and in vivo explant donor. The cytological and molecular analysis complemented and compared well and showed no genomic alterations in the plants regenerated through shoot bud differentiation. High multiplication frequency, molecular, cytological and phenotypic stability ensures the efficacy of the protocol developed for the production and conservation of this important endangered medicinal herb.

Asparagaceae↗
PubMed2006

In vitro propagation of an endangered medicinal plant Saussurea involucrata Kar. et Kir.

An efficient micropropagation system for Saussurea involucrata Kar. et Kir., an endangered Chinese medicinal plant, has been developed. Shoot organogenesis occurred from S. involucrata leaf explants inoculated on medium with appropriate supplements of plant growth regulators. 66.0% of shoot regeneration frequency and 5.2 shoots per leaf explant were achieved when cultured on a medium containing 10 microM 6-benzylaminopurine (BAP) and 2.5 microM 1-naphthaleneacetic acid (NAA). Shoot organogenesis was improved further when the leaf explants were pre-incubated at low temperature, and 80.6% of shoot regeneration frequency was recorded with 9.3 shoots per leaf explant at 4 degrees C by 5-day pretreatment period. Up to 87.0% of the regenerated shoots formed complete plantlets on a medium containing 2.5 microM indole-3-acetic acid (IAA) within 28 days, and 85.2% of the regenerated plantlets survived and grew vigorously in greenhouse condition. The phytochemical profile of the micropropagated plants was similar to that of wild plants. The regeneration protocol developed in this study provides a basis for germplasm conservation and for further investigation of medicinally active constituents of the elite medicinal plant.

Benzyl Compounds↗
PubMed2001

Microsporogenesis in the endangered species Cupressus dupreziana A. Camus: evidence for meiotic defects yielding unreduced and abortive pollen.

To understand the reproductive biology of Cupressus dupreziana A. Camus (Cupressaceae), a highly endangered Mediterranean conifer, the processes of microsporogenesis and pollen differentiation were investigated cytologically. Pre-meiotic development proved to be similar to the coniferous pattern: the microsporangia differentiated sporogenous tissue in which microsporocytes separated and underwent meiosis. As the meiotic steps proceeded, unexpected irregularities were observed concerning chromosomal and nuclear behaviour. This mainly included: abnormal chromosome segregation and cytokinesis, and nuclear fusion of the meiotic products. The result was the formation, in the same microsporangium, of heterogeneous microspore populations arranged in monads, dyads, triads, tetrads, and polyads, and cytoplasts giving rise to pollen grains of different sizes. This indicates that in C. dupreziana both abortive and unreduced pollen grains are generated. The significance of the finding is discussed in relation to reproductive biology and vulnerability to extinction.

Cell Differentiation↗
PubMed2004

Intraguild predation and interference competition on the endangered dragonfly Aeshna viridis.

We examined the effects of intraguild predation (IGP) and interference competition on an endangered dragonfly, Aeshna viridis Eversm. (Odonata: Anisoptera). A. viridis is rare in Europe due to the decrease in suitable habitats harboring the macrophyte Stratiotes aloides L. Stratiotes plants are the principal oviposition substrate for A. viridis females and protect the larvae of A. viridis from fish predation. In our study lakes A. viridis larvae are sympatric with larvae of Aeshna grandis and Aeshna juncea. The susceptibility of A. viridis larvae to IGP by similar-sized larvae of A. grandis and A. juncea was tested in a laboratory predation experiment. Microhabitat use of A. viridis and A. grandis was studied in the laboratory to determine the possible effects of interference competition on the spatial distribution of A. viridis larvae. Our results show that at least in laboratory conditions, A. viridis is susceptible to IGP and interference competition. In competition, A. grandis larvae dominated the middle and outer portion of S. aloides rosettes whereas A. viridis stayed in the inner parts. When A. grandis larvae were absent, A. viridis colonized the middle and outer parts of the rosettes. We conclude that asymmetric predation between odonate larvae of equal size can be intense, and that both IGP and interference competition affect A. viridis. Although natural habitat complexity diminishes their impact, these interactions may nevertheless influence the distribution of A. viridis in S. aloides waters and restrict its microhabitat use in S. aloides rosettes.

Animals↗
PubMed1999

Correlation of the combination of alcoholism and smoking with the occurrence of cancer in the oral cavity. A screening study in an endangered population.

A number of studies have previously been carried out on patients with tumors of the oral cavity, a majority of whom proved to be heavy smokers and heavy drinkers. However, we are not aware of literature reports relating to the converse situation: a study of alcoholics and strong smokers to establish the incidence of malignant processes of the oral cavity among them. Accordingly, the present aim was to investigate the occurrence of oral cavity lesions among 300 subjects who were alcoholic and heavy smokers and of the opinion that they had no tumor. Malignant processes were detected in the oral cavity or its environment in 2.66% of the 300 subjects, and more than 19% of them were found to harbour benign tumors and precancerous lesions. These investigations highlight the importance of screening examinations of the endangered population.

Adult↗
PubMed2005

Detection of low genetic variation in a critically endangered Chinese pine, Pinus squamata, using RAPD and ISSR markers.

With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (Ae) was 1.032, the percentage of polymorphic loci (P) was 6.45, and the expected heterozygosity (He) was 0.019 at the species level based on RAPD markers. The results of ISSR were consistent with those detected by RAPD but somewhat higher (I = 0.048, Ae = 1.042, P = 12.3, He = 0.029). The genetic variation of the subpopulation on the southwest-facing slope was much higher than that of the subpopulation on the northeast-facing slope, which may be attributed to the more diverse environment on the southwest-facing slope. The genetic differentiation between the two subpopulations was very low. The between-subpopulation variabilities, phiST, calculated from RAPD and ISSR data were 0.011 and 0.024. Because of the lack of fossil records and geological historical data, it was difficult to explain the extremely low genetic diversity of the species. We postulate that this ancient pine might have experienced strong bottlenecks during its long evolutionary history, which caused the loss of genetic variation. Genetic drift and inbreeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity. Human activities such as logging may have accelerated the loss of genetic diversity in P. squamata.

Conservation of Natural Resources↗
PubMed2005

Genetic structure of an endangered Portuguese semiferal pony breed, the Garrano.

The present study intends to survey the genetic variability of an endangered semiferal Portuguese native pony breed, the Garrano. Thirteen microsatellite markers were examined in 277 animals born in 1998, belonging to eight subpopulations corresponding to eight northern Portuguese geographic regions. Mean heterozygosity (H(o)) in the Garrano breed was 0.732, ranging from 0.531 to 0.857 across subpopulations. Allelic frequencies and diversity differed significantly between regions, suggesting the existence of genetic differentiation within the breed confirmed by the population differentiation estimator F(ST). Allele sharing genetic distance (Dps) was used to determine the relationship between the analyzed subpopulations, some of which are diverging significantly from the others. Relationships among six Iberian horse breeds (including the Garrano) were assessed through the restricted maximum likelihood method, which clusters the Garrano with another Celtic pony, the Spanish Asturcon, traditionally bred in geographical continuity with the Garrano. Results reveal a statistically significant deficit of heterozygotes within the Garrano breed (F(IT) = 0.031, p < 0.05). Regular monitoring should therefore be implemented so that the effect of genetic drift within subpopulations, enhanced by inbreeding, may be successfully minimized.

Alleles↗
PubMed2006

AFLP analysis of genetic diversity of the endangered species Sinopodophyllum hexandrum in the Tibetan region of Sichuan Province, China.

Amplified fragment length polymorphism (AFLP) markers were used to estimate the genetic diversity of seven wild populations of Sinopodophyllum hexandrum (Royle) Ying from the Tibetan region of Sichuan Province, China. Six primer combinations generated a total of 428 discernible DNA fragments, of which 111 were polymorphic. The percentage of polymorphic bands (PPB) was 25.93 at the species level, and PPB within population ranged from 4.91 to 12.38%. Genetic diversity (H(E)) within populations varied from 0.01 to 0.04, averaging 0.05 at the species level. As revealed by the results of AMOVA analysis, 58.8% of the genetic differentiation occurred between populations, and 41.2% within populations. The genetic differentiation was, perhaps, due to the limited gene flow (Nm = 0.43) of the species. The correlation coefficient (r) between genetic and geographical distance using Mantel's test for all populations was 0.698 (P = 0.014). The UPGMA cluster analysis revealed a similar result in that the genetic distances among the populations show, to a certain extent, a spatial pattern corresponding to their geographic locations. On the basis of the genetic and ecological information, we propose some appropriate strategies for conserving the endangered S. hexandrum in this region.

Berberidaceae↗
PubMed2006

Major histocompatibility complex variation in the endangered crested ibis Nipponia nippon and implications for reintroduction.

The major histocompatibility complex (MHC), with its extraordinary levels of genetic variation, is thought to be an essential aspect of the ability of an organism to recognize different parasites and pathogens. It has also been proposed to regulate reproductive processes in many aspects. Here we examine the genetic variation of the second exon of the MHC class II B genes of the crested ibis, an endangered species known to descend from just two breeding pairs rediscovered in 1981. Only five alleles are identified by single-strand conformation polymorphism (SSCP) analysis of 36 samples taken from both wild and captive populations, and a comparatively low level of divergence between MHC alleles is observed. We suggest that representative sampling of individuals with most of the different MHC allele genotypes to constitute a founder population, together with the monitoring of the pathogen status of candidate sites before release, is of great importance for raising the success rate of reintroduction for the crested ibis.

Amino Acid Sequence↗
PubMed2006

Genetic variability in Hesperozygis ringens Benth. (Lamiaceae), an endangered aromatic and medicinal plant of southern Brazil.

Hesperozygis ringens Benth. (Lamiaceae) is an aromatic and medicinal plant, characterized by a high concentration of isopulegone; it is endemic to the mountains of southeast Rio Grande do Sul, Brazil, and currently is considered endangered. The present study evaluated the intra- and interpopulation genetic variability of H. ringens by means of RAPD and ISSR molecular markers. The results showed that H. ringens populations are genetically structured, with low gene flow between populations, confirming the fragmentation imposed by anthropic action. Populations from the two areas of occurrence are genetically different. Low intrapopulation variability and heterozygosity were detected, indicating genetic drift and inbreeding. Based on the data, conservation strategies are discussed.

Base Sequence↗
PubMed2007

Patterns of genetic variation in Swertia przewalskii, an endangered endemic species of the Qinghai-Tibet Plateau.

Swertia przewalskii Pissjauk. (Gentianaceae) is a critically endangered and endemic plant of the Qinghai-Tibet Plateau in China. RAPD and ISSR analyses were carried out on a total of 63 individuals to assess the extent of genetic variation in the remaining three populations. Percentage of polymorphic bands was 94% (156 bands) for RAPD and 96% (222 bands) for ISSR. A pairwise distance measure calculated from the RAPD and ISSR data was used as input for analysis of molecular variance (AMOVA). AMOVA indicated that a high proportion of the total genetic variation (52% for RAPD and 56% for ISSR) was found among populations; pairwise Phi (ST) comparisons showed that the three populations examined were significantly different (p < 0.001). Significant genetic differentiation was found based on different measures (AMOVA and Hickory theta(B)) in S. przewalskii (0.52 on RAPD and 0.56 on ISSR; 0.46 on RAPD and 0.45 on ISSR). The differentiation of the populations corresponded to low average gene flow (0.28 based on RAPD and 0.31 based on ISSR), whereas genetic distance-based clustering and coalescent-based assignment analyses revealed significant genetic isolation among populations. Our results indicate that genetic diversity is independent of population size. We conclude that although sexual reproduction and gene flow between populations of S. przewalskii are very limited, they have preserved high levels of genetic diversity. The main factors responsible for the high level of difference among populations are the isolation and recent fragmentation under human disturbance.

China↗
PubMed2006

Monitoring of the endangered Pinna nobilis Linné, 1758 in the Mar Grande of Taranto (Ionian Sea, Italy).

The present study aimed to improve the knowledge of the bivalve Pinna nobilis L. population distribution in Mar Grande of Taranto (Ionian Sea). Although historical references report the local abundant presence of this endangered species, there is a lack of updated information about its exact distribution. For this purpose, a visual census of P. nobilis was performed by SCUBA diving in the Mar Grande basin from September 2004 to March 2005. Pinnids were found at depths from 3 to 16 m, with a density ranging from 0.1 to 0.7 ind ha(-1). The survey method employed in this study was non-destructive, relatively simple to perform and easily applicable for monitoring studies. Field data were stored in a database and linked with the study area by means of the GIS technology. The results of the present study indicate a tentative of recovery of P. nobilis population in Mar Grande in spite of all the difficulties of a degraded and heavily polluted environment and the damages of illegal fishing methods.

Animals↗
PubMed2006

Genetic diversity of the endangered Chinese endemic herb Primulina tabacum (Gesneriaceae) revealed by amplified fragment length polymorphism (AFLP).

Primulina tabacum Hance, is a critically endangered perennial endemic to limestone area in South China. Genetic variability within and among four extant populations of this species was assessed using AFLP markers. We expected a low genetic diversity level of this narrowly distributed species, but our results revealed that a high level of genetic diversity remains, both at population level (55.5% of markers polymorphic, H (E) = 0.220, I (S) = 0.321), and at species level (P = 85.6% of markers polymorphic, H (E) = 0.339, I (S) = 0.495), probably resulting from its refugial history and/or breeding system. High levels of genetic differentiation among populations was apparent based on Nei's genetic diversity analysis (G (st)=0.350). The restricted gene flow between populations is a potential reason for the high genetic differentiation. The population genetic diversity of P. tabacum revealed here has clear implications for conservation and management. To maintain present levels of genetic diversity, in situ conservation of all populations is necessary.

China↗