濒危物种巴东木莲的等位酶遗传多样性及其保护策略

为了确定中国特有濒危植物巴东木莲(Manglietia patungensis)的就地保护优先单元和制定迁地保护的取样策略,采用超薄平板聚丙烯酰胺等电聚焦电泳技术对巴东木莲的7个野生居群的等位酶遗传多样性及遗传结构进行了分析。通过对8个酶系统19个酶位点的分析结果来看,巴东木莲具有较高的遗传多样性和一定程度的遗传分化。每位点平均等位基因数（A）为1.57,多态位点百分率（P）为48.1%,平均预期杂合度（H_e）为0.192。巴东木莲居群间的遗传分化系数（G_ST）为0.165,说明其16.5％的遗传变异存在于居群间;基于遗传分化系数计算的基因流（N_m）为1.27,说明居群间存在适度的基因流;固定指数(F)为-0.191,显示巴东木莲居群杂合体轻微过量,纯合体略显不足。本研究表明,目前巴东木莲仍具有较高的遗传多样性并且在其适宜生境中可以完成自然更新,因此应采取以就地保护为主的综合保育策略。     

The importance of littoral forest remnants for indigenous bird conservation in southeastern Madagascar

The littoral forests of Madagascar are relatively unexplored ecosystems that are considered seriously threatened by deforestation and habitat fragmentation. We set out to describe the bird communities inhabiting the littoral forest remnants in three different sub-regions of southeastern Madagascar to determine the national importance of these forests for bird conservation. In total, 77 bird species were found inhabiting 14 littoral forest remnants. Of these species, 40 are endemic to Madagascar and a further 21 are endemic to the Indian Ocean sub-region, consisting of Madagascar, the Comoros and the Mascarenes. The matrix habitats (Melaleuca forests, marécage swamp forest, Eucalyptus plantations and Erica grassland) that immediately surround the littoral forests were depauperate of bird species and contained few species that were found within the littoral forests. The geographic location of littoral forest remnants had an important role in determining what bird species occurred within them, with the northern remnants having similar bird communities to nearby humid forest whilst the most southern remnant had a bird community that resembled those of nearby spiny forest habitats. Eleven bird species that have been previously described as being habitat-restricted endemics to either spiny forests or humid forests, were found in littoral forest remnants. These results suggest that these littoral forests may play an important transitional role between the two other major natural habitats (spiny forest and humid forest) of southeastern Madagascar. On this basis we advocate that the littoral forest remnants of southeastern Madagascar should be afforded continuing conservation priority.     

遗传多样性与濒危植物保护生物学研究进展

尽管对于濒危物种的遗传学人们已经进行了大量研究,但是种群遗传学在植物保护中的实际地位尚存在很大争议。濒危物种的遗传多样性可能会由于遗传漂变、近交的作用而丧失;但这种丧失更可能是濒危的结果而不是濒危的起因。遗传多样性水平与物种生存力之间没有任何必然的联系。但植物种群遗传结构如果由于自交不亲和等位基因的丧失和与亲缘种杂交造成的遗传同化而发生改变,那么它对物种生存力会产生明显负作用。     

Structure and genetic diversity of Ixora margaretae an endangered species

The dry forests of New Caledonia are an exceptional ecosystem because of their numerous endemic botanical species and their highly diversified fauna of insects, mollusks, reptiles and birds. Unfortunately, the area of the dry forests has been significantly reduced, mainly by human activities. Ecological, phenological and genetic analysis of Ixora margaretae, a symbolic species of the sclerophyll forest, has revealed contrasting traits among natural stands. The division of the natural range and then the separation of forest islands has greatly reduced the existing genetic variability of this species. The genetic diversity is strongly structured in genetic clusters which correspond well to specific ecotypes according to the environmental conditions and the forest types. Furthermore, genetic analysis of the reproductive and non-reproductive trees as well the half-sib families obtained by complete protection of mother trees has revealed substantial genetic drift which has resulted in increased loss of allelic variability. The total consumption of seeds by mainly rats confirms the observed absence of natural regeneration. All these results show that measures taken to protect the stands of dry forests will not be enough to maintain sufficient genetic variability of I. margaretae populations in the long term. Assisted regeneration with control of the increase in variability will be necessary to maintain the biodiversity of the species. The results obtained for I. margaretae must be confirmed with other symbolic species in order to take the necessary measures for the effective preservation of the dry forests in New Caledonia.     

Small effect of fragmentation on the genetic diversity of Dalbergia monticola, an endangered tree species of the eastern forest of Madagascar, detected by chloroplast and nuclear microsatellites

Background and Aims

The oriental forest ecosystem in Madagascar has been seriously impacted by fragmentation. The pattern of genetic diversity was analysed on a tree species, Dalbergia monticola, which plays an important economic role in Madagascar and is one of the many endangered tree species in the eastern forest.

Methods

Leaves from 546 individuals belonging to 18 small populations affected by different levels of fragmentation were genotyped using eight nuclear (nuc) and three chloroplast (cp) microsatellite markers.

Key Results

For nuclear microsatellites, allelic richness (R) and heterozygosity (H_e,nuc) differed between types of forest: R = 7·36 and R = 9·55, H_e,nuc = 0·64 and H_e,nuc = 0·80 in fragmented and non-fragmented forest, respectively, but the differences were not significant. Only the mean number of alleles (N_a,nuc) and the fixation index F_IS differed significantly: N_a,nuc = 9·41 and N_a,nuc = 13·18, F_IS = 0·06 and F_IS = 0·15 in fragmented and non-fragmented forests, respectively. For chloroplast microsatellites, estimated genetic diversity was higher in non-fragmented forest, but the difference was not significant. No recent bottleneck effect was detected for either population. Overall differentiation was low for nuclear microsatellites (F_ST,nuc = 0·08) and moderate for chloroplast microsatellites (F_ST,cp = 0·49). A clear relationship was observed between genetic and geographic distance (r = 0·42 P < 0·01 and r = 0·42 P = 0·03 for nuclear and chloroplast microsatellites, respectively), suggesting a pattern of isolation by distance. Analysis of population structure using the neighbor-joining method or Bayesian models separated southern populations from central and northern populations with nuclear microsatellites, and grouped the population according to regions with chloroplast microsatellites, but did not separate the fragmented populations.

Conclusions

Residual diversity and genetic structure of populations of D. monticola in Madagascar suggest a limited impact of fragmentation on molecular genetic parameters.     

Effects of forest management on mating patterns,pollen flow and intergenerational transfer of genetic diversity in wild Arabica coffee (Coffea arabica L.) from Afromontane rainforests

Coffea arabica, the wild ancestor of all commercial Arabica coffee cultivars worldwide, is endemic to the montane rainforests of Ethiopia. These forests, which harbour the most important C. arabica gene pool, are threatened by increasing anthropogenic disturbance, potentially altering the mating patterns, pollen dispersal and maintenance of genetic diversity in C. arabica understorey populations. We genotyped 376 adult coffee shrubs and 418 progenies from three natural unmanaged, and three highly managed coffee populations, using 24 microsatellite markers. Mating system analysis of C. arabica yielded an overall multilocus outcrossing rate of 76%, which contrasts with the common knowledge that C. arabica is a predominantly selfing species. In highly managed coffee populations, paternity could be assigned to 78% of the progenies, whereas in the unmanaged natural coffee populations, only 57% of the progenies could be assigned to a father, indicating reduced long‐distance pollen dispersal in managed forests. Furthermore, the fraction of selfed progenies was significantly higher in managed (23%) than unmanaged (10%) coffee forests. Finally, the lack of spatial genetic structure in all studied populations suggests high seed dispersal in unmanaged populations, and intense berry harvesting and coffee planting in the managed populations. Our results imply that in situ conservation of the wild gene pool of C. arabica must focus on limiting intensification of coffee forest management, as decreased pollen dispersal and increased selfing in C. arabica in intensively managed populations may increase the risk of genetic erosion. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 76–88.     

Phylogeographical patterns and genetic diversity in three species of Eurasian boreal forest beetles

Many species that occur in formerly glaciated areas of Fennoscandia have reached their current ranges from glacial refugial areas in Eurasia. Little is known of the refugia and postglacial colonization routes of insect species that are confined to boreal forests. Here, we investigate the phylogeography of three species of saproxylic beetles distributed across Eurasia: two rare boreal forest specialists, Pytho kolwensis and Pytho abieticola , and a common, less specialized species, Pytho depressus . In all species, there were two well-defined haplotype clades based on 645 bp of cytochrome oxidase subunit I gene sequence. In each species one clade was found only in China. The other clade occurred from China to north-western Europe in both P. kolwensis and P. depressus , but was apparently absent from China in P. abieticola. In spite of common phylogeographical patterns, the distribution of genetic variation differed markedly between the three species. In P. kolwensis , a highly-threatened species in old-growth forests in Fennoscandia, there was an extremely low level of genetic variation throughout Eurasia. One common haplotype, represented by 86% of the samples, dominated in all sampling localities. Levels of genetic variation were higher in both P. abieticola and P. depressus , with 31% and 58%, respectively, of the samples representing a unique haplotype. In each species, relationships between haplotypes were not well resolved, and haplotypes from one sampling locality were generally not clustered in either Neighbour-joining trees or statistical parsimony networks. These patterns in the distribution of genetic variation can be attributed to differences in the species' population sizes, ecologies, glacial refugial areas, and postglacial colonization dynamics.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 267–279.     

浙江省珍稀濒危植物物种多样性保护的关键区域

浙江省植物资源丰富,有野生维管植物215科1196属3283种,其中包含了我国特有属49个,浙江省特有植物约200余种,许多物种十分稀少,并受到严重威胁,亟待保护。但浙江省需优先保护的植物物种的分布并不是均匀的,有些地区的重要保护对象比较集中,对这些地区我们应该给予更多的保护。本文根据维管植物物种多样性、珍稀濒危植物的物种数量及个体数量特征、受威胁状况以及浙江省特有植物的分布情况,提出了浙江省珍稀濒危植物保护的7个关键区域：以西天目山为中心的浙西北山区,以古田山为中心的浙西山区,以九龙山为中心的浙西南山区,以凤阳山－百山祖为中心的浙南山区,以括苍山为中心的浙东山区,以天台山为中心的浙东丘陵,以普陀山为中心的舟山群岛。最后提出了浙江省植物物种多样性保护的几点建议。     

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north–south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north–south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics.     

Floral species richness,structural diversity and conservation value of vanilla agroecosystems in Madagascar

Agricultural landscapes provide financial livelihoods for farming communities in rural areas. However, such agroenvironments can significantly impact the local floral biodiversity and introduce harmful invasive species to the ecosystem. Despite the prominence of plantations throughout the tropics, their effects on local flora are limited to only a few specific cash crops and geographical regions. Here, we compared the species richness and structural diversity of vegetation in natural forest fragments and three types of vanilla plantation within the Sava region of north-east Madagascar ranging from those within or adjacent to existing forests, to intensively cultivated plantations. We recorded data on plant species abundance, diameter at breast height and canopy cover within multiple sites of each habitat. We used abundance data to calculate species richness indices, and we compared these metrics between habitats. Forested habitats contained a significantly higher floral species richness, structural diversity and more endemic and regionally native species than nonforested, anthropogenic vanilla plantations. However, our results suggest that the high floral species richness and structural diversity of natural forests can be partially achieved in vanilla plantations, depending on the site's management regime; traditionally managed vanilla plantations located close to natural forests can support diverse floral communities. These encouraging findings for plant conservation and sustainable agroforestry in Madagascar suggest that that newly created vanilla plantations and already existing nonforested plantations should endeavour to follow the more traditional forested approach to enhance the future sustainability and promote floristic diversity.     

Genetic diversity of Narcissus tortifolius,an endangered endemic species from Southeastern Spain

In this work, we analyzed inter-simple sequence repeat markers from 10 populations (298 individuals) spanning the whole distribution range of the endemic Narcissus tortifolius. We assessed genetic variation levels and distribution by estimates of genetic diversity, analysis of molecular variance (AMOVA), principal coordinates and Bayesian methods. N. tortifolius showed moderate genetic diversity at intrapopulation level and low genetic differentiation of populations. In general, Almerian populations showed slightly higher levels of genetic diversity than Murcian populations. Our results indicate that habitat fragmentation has not caused genetic depauperation in N. tortifolius but did reveal moderate genetic differentiation. Indeed, principal coordinate analysis and Mantel test revealed a slight tendency to separate populations into two groups (Murcian vs. Almerian). A recent isolation event of populations, together with the perennial nature of this species could be the main reasons for this low to moderate differentiation. Our findings could be used to establish management guidelines for the conservation of this rare species.     

Developing biological resource banks as a supporting tool for wildlife reproduction and conservation The Iberian lynx bank as a model for other endangered species

This work presents a Biological Resource Bank generated as a complementary supporting tool for the reproduction and the in situ and ex situ conservation of the Iberian lynx. In its design we prioritized the preservation of a maximum of the current genetic and biological diversity of the population, and the harmless collection of the samples. To provide future reproductive opportunities through any possible technique, we processed and cryopreserved germinal cells and tissues from dead animals, 7 males and 6 females, as well as somatic cells and tissues from 69 different individuals. This somatic cell reserve reflects a very important fraction of the population biodiversity which, furthermore, will allow the development of a wide variety of studies that can be easily extrapolated to the majority of the population. We have developed a new non-destructive method to isolate cells with stem-cell-like properties. If considered convenient in the future, and after proper research, such cells could permit therapeutic applications and perhaps be a good source to be used in somatic cell nuclear transfer. Samples of whole blood and its derivatives, hairs, urine and feces from many different individuals were also preserved. Proper storage of such samples is required to allow epidemiological studies to be performed for the testing of different etiological hypotheses or, in general, to develop any bio-sanitary study to improve conservation strategies within the natural habitat. This work describes the main aspects involved in the practical implementation of the Iberian lynx Biological Resource Bank, as a model that could be useful for the development of similar banks for other endangered species.     

A genetic diversity study of endangered Psiadia species endemic from Mauritius Island using PCR markers

The genus Psiadia Jacq. represents the most important indigenous genus, by the number of species present, in the Mascarene archipelago (Mauritius, Reunion, Rodrigues), and is a typical example of adaptive radiation in oceanic islands. The Mauritius species are used in traditional pharmacopoeia for their expectorant properties, and most of them are heavily threatened. Molecular genetic relationships between representatives of eight endangered endemic Psiadia species from Mauritius, conserved in Le Mondrain Reserve, and P. dentata (Cass.) DC, endemic from Reunion island, were studied. The absence of length variations of the 5s rDNA non-transcribed spacer demonstrated the recent common origin of all the species surveyed. RAPD analysis revealed a relatively high intra-specific variability in accordance with the outcrossing mode of reproduction of Psiadia species. Moreover, RAPD analysis showed the existence of four major phenetic groups: (A) P. arguta (Pers.) Voigt, P. dentata, (B) P. penninervia D. C., P. terebinthina A.J. Scott, P. lithospermifolia (Lam.) Cordem, (C) P. viscosa (Lam.) A.J. Scott, P. canescens A.J. Scott, P. cataractae A.J. Scott, and (D) P. pollicina A.J. Scott. These groups were consistent with the chemical composition of the essential oils of the species as well as with their floral characteristics, based on literature. A molecular germplasm database for Psiadia species was established, which will allow further characterisation of new samples being introduced in Le Mondrain Reserve for conservation purpose.     

Assessing genetic diversity for conservation management: a case study of a threatened reptile

The consequences of inbreeding in small isolated populations are well documented, yet populations are often managed in isolation to avoid irreversibly mixing genetic lineages and to maintain the historic integrity of each population. Three remaining populations of Whitaker's skink ( Cyclodina whitakeri ) in New Zealand, remnants of a once wider distribution, illustrate the conflict between this genetic goal (separate management of populations) with the more tangible and immediate threats of small population size and inbreeding. Middle and Castle Islands harbour populations of C. whitakeri and have been separated from each other and from the mainland for ∼10 000 years. The single mainland population at Pukerua Bay is extremely small, declining and deemed a high priority for management. We sequenced a 550 bp region of mitochondrial DNA (mtDNA,ND2) and genotyped animals from all three populations at 13 microsatellite loci. The population of C. whitakeri at Pukerua Bay showed marked differences from the island populations at both mtDNA (unique, fixed haplotype) and microsatellite loci ( F _ST∼0.20), and private alleles were detected at a high frequency (24% of all alleles). However, we attribute this pattern to an historic genetic gradient coupled with rapid genetic drift. Further, animals in captivity show genetic signatures of both Pukerua Bay and island populations, despite the goal to maintain a pure Pukerua Bay stock. The mixed genetic stock in captivity provides an opportunity for the addition of skinks from Middle Island to evaluate the risks of further population hybridization, including the disruption of potential local adaptation, while mitigating the risks of inbreeding.     

Adaptive genetic diversity of trees for forest conservation in a future climate: a case study on Norway spruce in Austria

Genetic resources of forest trees are considered as a key factor for the persistence of forest ecosystems because the ability of tree species to survive under changing climate depends strongly on their intraspecific variation in climate response. Therefore, utilizing available genetic variation in climate response and planting alternative provenances suitable for future climatic conditions is considered as an important adaptation measure for forestry. On the other hand, the distribution of adaptive genetic diversity of many tree species is still unknown and the predicted shift of ecological zones and species’ distribution may threaten forest genetic resources that are important for adaptation. Here, we use Norway spruce in Austria as a case study to demonstrate the genetic variation in climate response and to analyse the existing network of genetic conservation units for its effectiveness to safeguard the hotspots of adaptive and neutral genetic diversity of this species. An analysis of the climate response of 480 provenances, clustered into 9 groups of climatically similar provenances, revealed high variation among provenance groups. The most productive and promising provenance clusters for future climates originate from three regions that today depict the warmest and driest areas of the natural spruce distribution in Austria. Gap analysis of the Austrian genetic conservation units in the EUFGIS Portal suggests adequate coverage of the genetic hotspots in southern parts of Austria, but not in eastern and northern Austria. Therefore conservation measures and sustainable utilization of the valuable genetic resources in these regions need to be expanded to cover their high adaptive genetic variation and local adaptation to a warmer climate. The study shows that current conservation efforts need to be evaluated for their effectiveness to protect genetic resources that are important for the survival of trees in a future climate.     

Globally common,locally rare: revisiting disregarded genetic diversity for conservation planning of widespread species

Species endangerment, as determined by the national and international authorities, are crucial in conservation decisions at local and regional scales. While species are the priority unit of conservation, the subspecies of widespread species are often neglected in conservation planning and research, irrespective of their unique genetic identity. Peripheral populations of widespread species are often isolated and endangered while their status on the IUCN Red List is considered as ‘Least Concern’. We advocate for the evaluation of widespread polytypic species, and to recognize the importance of assessing intraspecific populations that are distinct from the distribution of widespread species.     

Landscape connectivity of Cercidiphyllum japonicum,an endangered species and its implications for conservation

Cercidiphyllum japonicum, a Tertiary relict, recolonized areas north of the Yangtze River after the last glacial; however, little is known about its specific colonization corridors. Together with distribution models, the least cost path (LCP) analysis has been used to reveal the landscape connectivity of species. In this study, we utilized the categorical LCP method, combining the species distribution with genetic data from cpDNA and nuclear markers, to identify the possible dispersal routes of C. japonicum after the LGM. Across time periods and genetic markers, the results revealed that the species generally spread from the western edge of the Sichuan Basin, while the highest degree of dispersal potential corresponds with the year 2080 and the cpDNA haplotype. Furthermore, shifts in the species' range and the indication of an area of low genetic divergence further support the existence of a dispersal corridor. Overall, we believe that a dispersal route from the western edge of the Sichuan Basin through the Qinling Mountains and further to the northeast could exist, and therefore, the results are an important supplement to the evolutionary history of C. japonicum. In the future, we believe species distribution models (SDM) and connectivity assessment in relation to climate change will provide increasingly useful information and new implications for prioritizing the conservation of the endangered species.     

Evaluating species nonmonophyly as a trait affecting genetic diversity: a case study of three endangered species of Antirrhinum L. (Scrophulariaceae)

Molecular markers are routinely used to assess levels of diversity within and among populations, particularly with regard to species of conservation concern. However, when interpreting the level and partitioning of diversity observed, an implicit assumption is often made that the populations of the species in question form a monophyletic group. We tested this assumption in three endemics of Antirrhinum (A. charidemi, A. subbaeticum, and A. valentinum) using 79 nuclear [internal transcribed spacer (ITS)] and 85 plastid (psbA-trnH, trnT-trnL, trnK-matK, trnS-trnG) sequences representing multiple accessions of each of 24 Antirrhinum species (single accession of A. cirrhigerum). These species share six life history traits implicated in levels of genetic diversity, and have been the subject of previous population genetic studies. Populations of all three species formed monophyletic groups on ITS analysis. In contrast, none of the three species formed monophyletic groups on plastid sequence analysis: populations of A. charidemi fall in a monophyletic group including one accession of A. mollissimum, populations of A. subbaeticum form a polyphyletic group with plastid sequences shared with A. pulverulentum, and populations of A. valentinum are unresolved within a clade containing six other species. Lack of monophyly using plastid sequences is interpreted as a combination of shared ancestral polymorphism and hybridization in a reticulate evolutionary history of these species. Monophyly in the ITS tree may reflect a more recent sequence homogenization. We draw attention to the evaluation of species monophyly alongside the contribution of other life history traits in the historical interpretation of the level and partitioning of genetic diversity, and its use in recommendations for species conservation programs.