分子标记在家畜遗传多样性研究中的应用

家畜遗传多样性是生物多样性的重要组成部分,与人类未来的生存与发展密切相关。中国拥有丰富的地方家畜品种资源,但由于保种不当和盲目引进外来品种进行杂交、资金缺乏等原因,许多品种已濒临灭绝。如何保存利用好我国优良的家畜遗传资源已成为越来越严峻的问题。随着生物学技术的不断发展与完善,许多分子标记技术已经应用于畜禽遗传资源的研究。简要介绍了在家畜遗传多样性研究中应用最广的几种分子标记及其特性,讨论了在家畜遗传多样性的研究中如何选用适当的分子标记。     

The potential role of arbuscular mycorrhizal fungi in protecting endangered plants and habitats

Ecosystems worldwide are threatened with the extinction of plants and, at the same time, invasion by new species. Plant invasiveness and loss of species can be caused by similar but opposing pressures on the community structures. Arbuscular mycorrhizal fungi (AMF) can have multiple positive effects on plant growth, productivity, health, and stress relief. Many endangered species live in symbiosis with AMF. However, the list of the International Union for Conservation of Nature and Natural Resources (IUCN Red List of Threatened Species) indicates that the mycorrhizal status of most of the threatened species has not been assessed. Rare plants often occur in specialized and also endangered habitats and might utilize specialized or unique AMF. The specificity of any endangered plant to its AMF population has not been investigated. Because most of the current AMF isolates that are available colonize a broad range of plant species, selected inocula could be used to promote growth of endangered plants before the proper and more effective indigenous AMF are characterized. Application of AMF in field sites to protect endangered plants is hardly feasible due to the complexity of plant community structures and the large amount of fungal inocula needed. Endangered plants could, however, be grown as greenhouse cultures together with appropriate fungi, and, at the relevant developmental stage, they could be re-planted into native sites to prevent extinction and to preserve plant community ecology.     

滇池土著鱼类现状

于2000年4月－12月对滇池区域的土著鱼类进行调查发现,滇池土著鱼类由20世纪60年代的26种减少到目前的11种,这11种滇池土著鱼类中,仅有4种生活于滇池湖体,其余7种均生活于滇池湖周一些溪流的上游或溶洞中,通过对土著鱼类及其栖息地的实地调查并结合文献资料,分析了滇池土著鱼类多样性的历史变化,各种类在空间上的变化方式以及滇池土著鱼类多样性迅速降低的原因,并就保护滇池土著鱼类提出具体的解决方法和途径。     

Restricted dispersal and genetic diversity in populations of an endangered montane lizard (Eulamprus leuraensis,Scincidae)

Many alpine species are under threat from global climate change, as their geographic ranges become increasingly fragmented and unsuitable. Understanding rates and determinants of gene flow among such fragmented populations, over historical as well as recent timescales, can help to identify populations under threat. It is also important to clarify the degree to which loss of local populations reduces overall genetic diversity within the taxon. The endangered Blue Mountains Water Skink (Eulamprus leuraensis) is restricted to <40 small swamps in montane south‐eastern Australia. Our analyses of seven microsatellite loci of 241 animals from 13 populations show strong geographic structure, with major genetic divergence even between populations separated by <0.5 km. Dispersal between populations is scarce, and appears to involve mostly males. Our analyses suggest potential recent bottleneck events in all the identified populations, and lower genetic diversity and population size parameter at lower‐elevation sites than at higher‐elevation sites. Management of this endangered taxon thus needs to treat most populations separately, because of their genetic distinctiveness and low rates of genetic exchange.     

Halting indigenous biodiversity decline: ambiguity, equity, and outcomes in RMA assessment of significance

In New Zealand, assessment of ?significance? is undertaken to give effect to a legal requirement for local authorities to provide for protection of significant sites under the Resource Management Act (1991). The ambiguity of the statute enables different interests to define significance according to their goals: vested interests (developers), local authorities, and non-vested interests in pursuit of protection of environmental public goods may advance different definitions. We examine two sets of criteria used for assessment of significance for biological diversity under the Act. Criteria adapted from the 1980s Protected Natural Areas Programme are inadequate to achieve the maintenance of biological diversity if ranking is used to identify only highest priority sites. Norton and Roper-Lindsay (2004) propose a narrow definition of significance and criteria that identify only a few high-quality sites as significant. Both sets are likely to serve the interests of developers and local authorities, but place the penalty of uncertainty on non-vested interests seeking to maintain biological diversity, and are likely to exacerbate the decline of biological diversity and the loss of landscape-scale processes required for its persistence. When adopting criteria for assessment of significance, we suggest local authorities should consider whose interests are served by different criteria sets, and who will bear the penalty of uncertainty regarding biological diversity outcomes. They should also ask whether significance criteria are adequate, and sufficiently robust to the uncertainty inherent in the assessment of natural values, to halt the decline of indigenous biological diversity.     

濒危兰科植物再引入技术及其应用

稀有、濒危植物的再引入,是在条件成熟时,把经过迁地保护的人工繁殖体重新放回到它们原来自然和半自然的生态系统或适合它们生存的野外环境中去,重建较为完善的生态系统。再引入技术的目标在于提高生态系统生物多样性及群落稳定性,建立可自我维持种群,它是继就地保护和迁地保护等保护策略之外的一种新兴的珍稀濒危植物保育方式。国际上再引入技术的研究刚起步,高度成功的还不多,目前可借鉴的成熟经验较少。通过分析国内外已经开展的若干珍稀濒危植物再引入技术案例,重点介绍国内外濒危兰科植物再引入的研究现状、技术体系和评价标准,讨论了再引入技术的类型和方法,并总结了可能影响再引入成败的制约性因素,分析了适用于兰科植物的再引入技术要素。由此提出濒危兰科植物再引入的重要现实意义,为今后的规模化人工栽培提供科学依据,同时有利于指导其他濒危植物再引入技术规程的制定。     

Evaluating costs for the <Emphasis Type="Italic">in vitro</Emphasis> propagation and preservation of endangered plants

In vitro methods provide opportunities for propagating and preserving endangered plant species when seed-based methods are not adequate. Such species include those that produce few or no seeds, as well as species with recalcitrant seeds. Tissue culture propagation methods can be used to produce such plants for reintroduction, research, education, display, and commerce. They can also be the basis for tissue banking as a way to preserve genetic diversity when seeds cannot be banked. With some recalcitrant species, embryo banking, a method which also utilizes in vitro culture for recovery germination, is possible. The number of endangered species that will require in vitro methods is estimated to be at least 5,000 worldwide. Further information is needed to identify these species, and the ongoing collection of information into databases on endangered species and recalcitrant species will help provide this. The costs of these methods are higher than for traditional propagation and preservation, but they may be necessary for species under higher threat. The multiplication rate of a culture, as well as the rates of rooting and acclimatization, has a major effect on the number of transfers needed for producing plants or tissue for banking, and improvements that will increase the efficiency of these steps can help lower costs. Further research into factors affecting the growth of tissues in vitro, as well as coordination of efforts among institutions with infrastructure for in vitro work, should facilitate the application of in vitro methods to the endangered species that cannot be propagated or preserved using seeds.     

Structural analysis, identification, and design of calcium-binding sites in proteins

Assigning proteins with functions based on the 3-D structure requires high-speed techniques to make a systematic survey of protein structures. Calcium regulates many biological systems by binding numerous proteins in different biological environments. Despite the great diversity in the composition of ligand residues and bond angles and lengths of calcium-binding sites, our structural analysis of 11 calcium-binding sites in different classes of proteins has shown that common local structural parameters can be used to identify and design calcium-binding proteins. Natural calcium-binding sites in both EF-hand proteins and non-EF-hand proteins can be described with the smallest deviation from the geometry of an ideal pentagonal bipyramid. Further, two different magnesium-binding sites in parvalbumin and calbindin(D9K) can also be identified using an octahedral geometry. Using the established method, we have designed de novo calcium-binding sites into the scaffold of non-calcium-binding proteins CD2 and Rop. Our results suggest that it is possible to identify calcium- and magnesium-binding sites in proteins and design de novo metal-binding sites.     

Bird naming systems by Akan people in Ghana follow scientific nomenclature with potentials for conservation monitoring

Background

Studies on indigenous knowledge of fauna particular birds and its potential use in biodiversity conservation and management are rare globally. Characteristics used in creating indigenous bird names in many Ghanaian languages are undocumented. The main aim of this study is to answer the question “whether indigenous bird naming systems by the Akan tribes in Ghana follow scientific nomenclature and whether indigenous Akan bird knowledge can potentially help improve bird conservation efforts in Ghana.

Methods

Purposive sampling technique was employed in selecting 10 respondents from 25 communities in the five administrative districts in the Central Region. The study was conducted between November 2014 and March 2015. A mixed method approach was adopted in the data collection including key person interviews, focus group discussion, and structured interview supported by a participatory field observation.

Results

Indigenous people in the study area have reported 143 species of birds belonging to 44 families representing 57 % of total number of species with known local names in Ghana. The study revealed that just as Latin and common English naming systems, indigenous Akan bird names originated from features of the bird, including plumage, vocalizations or behavioural characteristics and belief systems of the indigenous people. The study also discovered that indigenous people in the study area have distinct names for different species within a particular family for most of the birds they could identify. However, they occasionally assign a single general name for either the entire family or all species therein.

Conclusions

The study found evidence to support the prediction that indigenous bird naming systems in the Akan language follow scientific nomenclature. Indigenous knowledge and understanding of birds in the study area can be tapped and used in conservation planning and monitoring of birds. This research thus provides sufficient evidence to prove that indigenous knowledge by the Akan tribes in the study area can be useful in bird conservation and monitoring programs in Ghana. Further research in other Ghanaian languages is recommended.

     

Conservation genetics of freshwater fish

Genetic markers have helped to resolve many difficult taxonomic problems and map patterns of diversity within and among remnant populations of threatened and endangered species. Knowledge of historical patterns of gene flow can help to manage dispersal among anthropogenically fragmented populations. Genetic considerations are used in the design of captive breeding programmes that avoid inbreeding depression and artificial selection that may impact on Darwinian fitness. Case studies from endangered populations of topminnows from North American deserts are used to illustrate a variety of methods used in conservation genetic studies. Several merits of studying putatively neutral, molecular markers v. adaptive phenotypic traits are discussed.     

Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago

During the late nineteenth century, Europeans introduced rabbits to many of the sub-Antarctic islands, environments that prior to this had been devoid of mammalian herbivores. The impacts of rabbits on indigenous ecosystems are well studied; notably, they cause dramatic changes in plant communities and promote soil erosion. However, the responses of fungal communities to such biotic disturbances remain unexplored. We used metabarcoding of soil extracellular DNA to assess the diversity of plant and fungal communities at sites on the sub-Antarctic Kerguelen Islands with contrasting histories of disturbance by rabbits. Our results suggest that on these islands, the simplification of plant communities and increased erosion resulting from the introduction of rabbits have driven compositional changes, including diversity reductions, in indigenous soil fungal communities. Moreover, there is no indication of recovery at sites from which rabbits were removed 20 years ago. These results imply that introduced herbivores have long-lasting and multifaceted effects on fungal biodiversity as well as highlight the low resiliency of sub-Antarctic ecosystems.     

Can we bring Madagascar's critically endangered palms back from the brink? Genetics,ecology and conservation of the critically endangered palm Beccariophoenix madagascariensis

Madagascar has a highly distinctive flora and is one of the world biodiversity hot spots. There are more than 170 species of palms, the majority of which are vulnerable, endangered or critically endangered endemics. Palms are utilized for many human uses, many of which lead to plant death or seed harvesting. Combined with reduced populations resulting from extensive forest clearing, those species which are harvested from the wild are under additional threat of extinction. Species recovery programmes have the potential to save some of the most iconic species before it is too late. This study documented the current known populations of the critically endangered palm Beccariophoenix madagascariensis, a species utilized for both local and international purposes. The study specifically investigated the genetic diversity and inbreeding within populations and the potential differentiation between populations and with the newly described species B. alfredii . We found that despite critically small population sizes there was considerable genetic diversity within populations. We also found that ecologically and or geographically distinct populations were genetically distinct. Populations within 3 km of each other exhibited considerable gene flow, probably owing to seed dispersal. The populations were inbred but reproductive viability had been maintained. Conservation and recovery options are discussed. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 589–608.     

Insect diversity and trophic structure differ on native and non‐indigenous congeneric rushes in coastal salt marshes

Displacement of native plant species by non‐indigenous congeners may affect associated faunal assemblages. In endangered salt marshes of south‐east Australia, the non‐indigenous rush Juncus acutus is currently displacing the native rush Juncus kraussii, which is a dominant habitat‐forming species along the upper border of coastal salt marshes. We sampled insect assemblages on multiple plants of these congeneric rushes in coastal salt marshes in Sydney, New South Wales, Australia, and compared the abundance, richness, diversity, composition and trophic structure between: (i) J. acutus and J. kraussii at invaded locations; and (ii) J. kraussii at locations either invaded or not invaded by J. acutus. Although J. acutus supported a diverse suite of insects, species richness and diversity were significantly greater on the native J. kraussii. Moreover, insect assemblages associated with J. kraussii at sites invaded by J. acutus were significantly different from, and more variable than, those on J. kraussii at non‐invaded sites. The trophic structure of the insect assemblages was also different, including the abundance and richness of predators and herbivores, suggesting that J. acutus may be altering consumer interactions, and may be spreading in part because of a reduction in herbivory. This strongly suggests that J. acutus is not playing a functionally similar role to J. kraussii with respect to the plant‐associated insect species assemblages. Consequently, at sites where this non‐indigenous species successfully displaces the native congener, this may have important ecological consequences for community composition and functioning of these endangered coastal salt marshes.     

Life-history and habitat features influence the within-river genetic structure of Atlantic salmon

Defining populations and identifying ecological and life-history characteristics affecting genetic structure is important for understanding species biology and hence, for managing threatened or endangered species or populations. In this study, populations of the world's largest indigenous Atlantic salmon (Salmo salar) stock were first inferred using model-based clustering methods, following which life-history and habitat variables best predicting the genetic diversity of populations were identified. This study revealed that natal homing of Atlantic salmon within the Teno River system is accurate at least to the tributary level. Generally, defining populations by main tributaries was observed to be a reasonable approach in this large river system, whereas in the mainstem of the river, the number of inferred populations was fewer than the number of distinct sampling sites. Mainstem and headwater populations were genetically more diverse and less diverged, while each tributary fostered a distinct population with high genetic differentiation and lower genetic diversity. Population structure and variation in genetic diversity among populations were poorly explained by geographical distance. In contrast, age-structure, as estimated by the proportion of multisea-winter spawners, was the most predictive variable in explaining the variation in the genetic diversity of the populations. This observation, being in agreement with theoretical predictions, emphasizes the essence of large multisea-winter females in maintaining the genetic diversity of populations. In addition, the unique genetic diversity of populations, as estimated by private allele richness, was affected by the ease of accessibility of a site, with more difficult to access sites having lower unique genetic diversity. Our results show that despite this species' high capacity for migration, tributaries foster relatively closed populations with little gene flow which will be important to consider when developing management strategies for the system.     

Evaluation of floristic diversity in urban areas as a basis for habitat management

Questions: How can floristic diversity be evaluated in conser‐vation plans to identify sites of highest interest for biodiversity? What are the mechanisms influencing the distribution of species in human‐dominated environments? What are the best criteria to identify sites where active urban management is most likely to enhance floristic diversity? Location: The Hauts‐de‐Seine district bordering Paris, France. Methods: We described the floristic diversity in one of the most urbanized French districts through the inventory of ca. 1000 sites located in 23 habitats. We built a new index of floristic interest (IFI), integrating information on richness, indigeneity, typicality and rarity of species, to identify sites and habitats of highest interest for conservation. Finally, we explored the relationship between site IFI and land use patterns (LUP). Results: We observed a total of 626 vascular plant species. Habitats with highest IFI were typically situated in seminatural environments or environments with moderate human impact. We also showed that neighbouring (urban) structures had a significant influence on the floristic interest of sites: for example, the presence of collective dwellings around a site had a strong negative impact on IFI. Conclusions: Our approach can be used to optimize management in urban zones; we illustrate such possibilities by defining a ‘Site Potential Value’, which was then compared with the observed IFI, to identify areas (e.g. river banks) where better management could improve the district's biodiversity.     

A parasite-driven wedge: infectious diseases may explain language and other biodiversity

Parasite–host coevolutionary races are spatially variable across species' or human cultural ranges. Assortative sociality, biased toward local conspecifics, and limited dispersal (philopatry) in humans and other organisms can be adaptive through reduced contact with dangerous contagions harbored by distant/non-local conspecifics. These factors can generate cultural or population divergence. Thus, parasites are like a wedge driving groups apart through their effective creation of anticontagion behaviors. If this proposition is correct, then biological diversity should positively correlate with parasite diversity. Here we show that the worldwide distribution of indigenous human language diversity, a form of biodiversity, is strongly, positively related to human parasite diversity indicative of a legacy of parasite-mediated diversification. The significant pattern remains when potential confounds are removed. The pattern too is seen in each of the six world regions and is not confounded by regional differences in their history of colonization and conquest. We hypothesize that variation in limited dispersal and assortative sociality with conspecifics in response to the worldwide spatial variation in pathogen diversity provides a fundamental mechanism of population divergence explaining many important aspects of the geographic patterns of biodiversity. This hypothesis has broad implications for a diversity of research topics including language diversity, cultural evolution, speciation, phylogeny and biogeography.     

Effect of alien riparian vegetation and its removal on a highly endemic river macroinvertebrate community

Invasive alien trees along river banks can reduce indigenous biodiversity, while their removal can restore it. We assessed here family- and species-level responses of river benthic macroinvertebrate assemblages to three riparian vegetation types (natural, alien trees, cleared of alien trees) in the Cape Floristic Region biodiversity hotspot. High species beta diversity of this highly endemic fauna meant that between-river, as well as seasonal effects, dominated assemblage patterns. SASS5, a qualitative, rapid bioassessment technique, based on the sensitivity of the families present, was used as a measure of river health and, indirectly, of water quality. SASS indicated a decline in water quality conditions after alien clearing, a likely response to the greater insolation and apparent erosion of cleared banks, resulting in elevated temperatures and suspended solids and lowered oxygen levels. Overall, cleared and natural sites were more similar to each other than to alien sites, suggesting some post-clearing recovery. However, many sensitive, endemic taxa survived in alien-invaded sites, and more than in the natural sites. These endemic species made use of shady, cool, high-oxygen levels under the alien tree canopy. However, endemics declined in overall abundance in sites cleared of aliens, being replaced by more tolerant, widespread taxa. Clearance of the alien trees opened up the rivers to sunny conditions, which had a major impact on community composition. Vegetation types, oxygen levels and river width were important environmental variables affecting these macroinvertebrate responses. Re-establishment of invertebrate biodiversity matched that of indigenous vegetation, with the most sensitive endemic taxa only recovering after establishment of bushy indigenous and shade-producing fynbos. Therefore, for biodiversity conservation objectives to be achieved, it is essential that indigenous plants are maintained and encouraged during and after clearing to ensure the recovery of endemic and sensitive taxa.     

Studying Cultural Evolution at the Tips: Human Cross-cultural Ecology

While human genetic variation is limited due to a bottleneck on the origin of the species ～200 kya, cultural traits can change more rapidly, and may do so in response to the variation in human habitats. Does cultural diversification simulate a natural experiment in evolution much like biodiversity so that cultural divergences and convergences can be interpreted in terms of the differences and similarities of local environments? Or is cultural diversity simply the result of human behavioral flexibility? Although the majority of cultural data comes from the tips of the hominin phylogeny, anthropologists can follow the example of evolutionary ecologists, who often compare the endpoints of phylogenies when that is all that is available. This article compares 97 contemporary indigenous language communities from around the world, and 24 of their cultural traditions, to help determine whether human cultures and their cultural traits are proportionately dispersed, as predicted by the neutral theory of biodiversity, or whether they show non-proportionalities that could be explained with evolutionary reasoning.     

Threat categorisation and conservation prioritisation of floristic diversity in the Indian Himalayan region: A state of art approach from Manali Wildlife Sanctuary

Strategies have been suggested by many conservationists to conserve biodiversity at regional, national and global levels. However, conservation strategies developed in the past were mostly based on qualitative attributes or one or two attributes. In the Himalayan region biodiversity varies from aspect to aspect, habitat to habitat and community to community therefore, location specific studies are required for its conservation and management. In the present study an approach has been developed to prioritise species at local level using six conservation attributes. Threat categorisation of the floristic diversity was undertaken based on Conservation Priority Index. Of the total 637 species of vascular plants recorded, 10 species were categorised as critically endangered; 15 species as endangered and 31 species as vulnerable. Two species as critically endangered, seven species as endangered and three species as vulnerable according to IUCN have been also recorded which indicated the importance of the sanctuary. Maximum threatened species were found in altitudinal zones 2000–2800 m and sites dominated by Betula utilis and Rhododendron campanulatum in forest and alpine zones, respectively. The two factors of over exploitation and habitat degradation have been identified as major threats to the floristic diversity. Therefore, monitoring of population and habitats, development of conventional protocol; establishment of species in-situ conditions and akin habitats and replication of this approach in other parts of Indian Himalayan Region have been suggested.