ConGRESS genetics

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ConGRESS (Conservation Genetic Resources for Effective Species Survival) is an EU consortium dedicated to transferring current knowledge in conservation genetics and in the analysis of genetic variation data to management professionals and policy makers. ConGRESS is funded by the Seventh Framework Programme (FP7) of European Commission.

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  • ConGRESS (Conservation Genetic Resources for Effective Species Survival) is an EU consortium dedicated to transferring current knowledge in conservation genetics and in the analysis of genetic variation data to management professionals and policy makers. ConGRESS is funded by the Seventh Framework Programme (FP7) of EuropeanCommission.This presentation will give you an overview of conservation genetics – a new field of research and a practical tool for effective biodiversity management and species survival.
  • Firstly, I will briefly introduce why genetic diversity is politically important and describe the field that studies it, conservation genetics. Secondly, I will describe in detail what genetic diversity is. Thirdly, I will I will move on to introduce what high and low genetic diversity mean for biodiversity and finally, we will see examples of recent studies and practical genetic tools used in the field.
  • The Convention on Biological Diversity (CBD) is founded on the principle that biological diversity is comprised of ―genetic differences within species, the diversity of species and the variety of ecosystems. In other words, genetic diversity is seen as one of the three levels that make up biodiversity, the other levels being diversity between species and ecosystems.
  • However, in the European biodiversity policy,the diversity of species and the variety of ecosystems have been emphasised, but the Habitats Directive, the corner stone of Europe’s nature conservation policy, does not directly refer to genetic differences within species. Only the article 10 advices member states “to encourage the management of features of the landscape which are of major importance for wild fauna and flora”. Those features include the genetic exchange of wild species.According to the Habitat’s Directive Article 1i, the conservation status of species will be taken as "favourable" when:- population dynamics data on the species concerned indicate that it is maintaining itself on a long-term basis as a viable component of its natural habitats, and- the natural range of the species is neither being reduced nor is likely to be reduced for the foreseeable future, and- there is, and will probably continue to be, a sufficiently large habitat to maintain its populations on a long-term basis;In the United States, the Endangered Species Act is more precise: it defines the term species to include any subspecies of fish or wildlife or plants, and any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature (ESA: 1973, amended through the 108th Congress 2003). Therefore, it recognises the importance of the most fundamental building blocks of adaptive evolution: genetic variation within species.Read more:European Commission (1992) Council Directive 92/43/EEC of 21 May 1992 on the conservation of natural habitats and of wild fauna and flora. Available in: http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=CELEX:31992L0043:EN:NOTDepartment of the Interior, U.S. Fish and Wildlife Service (1973) ENDANGERED SPECIES ACT OF 1973, As Amended through the 108th Congress. Available in: http://www.nmfs.noaa.gov/pr/pdfs/laws/esa.pdf
  • As we have seen, biodiversity policy faces severe challenges. In Europe, the definition of Favourable Conservation Statushas been underintensepolitical and scientificdiscussion. Can we improve the measures of biodiversity management – and finally be able to ensure the viability of species in their natural range in a long term basis, as the Habitats Directive requires?Conservation genetics is a field of biology that uses genetic information to help conserve and manage natural populations. Within the scientific community, there is broad consensus that genetic diversity is important for both the short- and long-term viability and future evolution of populations. Genetic diversity is a buffer against population crashes in environmental changes. In the long term, genetic diversity is the raw material for evolution. The Habitats Directive stresses the necessity of research in order to implement meaningful species conservation measures. From the point of view of conservation genetics, the latest research results not been fully implemented in legislation. Read more:Laikre Linda, Nilsson Torbjörn, Primmer Craig R., Ryman Nils, and Allendorf Fred W. (2009)Importance of Genetics in the Interpretation of Favourable Conservation Status. Conservation BiologyVolume 23, No. 6, 1378–1381.
  • Genetic diversity is, however, a strongly emerging aspect in current biodiversity policy.In 2010 at Nagoya, a revised and updated Strategic Plan for Biodiversity was adopted by the CBD Parties for the 2011-2020 period. The plan includes the Aichi Biodiversity Targets, wheregenetic diversity is included in the Strategic Goal C. A commitment is sought to safeguard genetic diversity and to halt the genetic erosion of species as far as possible.The EU biodiversity strategy to 2020 published in 2011, also recognizes that the innovation potential of genetic diversity in ecosystem restoration is largely untapped. According to this strategy,in the EU, only 17 % of habitats and species and 11 % of key ecosystems protected under EU legislation are in a favourable state. This is in spite of action taken to combat biodiversity loss, particularly since the EU 2010 biodiversity target was set in 2001.The Habitats Directive Article 17 requires Member States to report every six years about the progress made with the implementation of the Habitats Directive - the present reporting period ends in 2012. Explanatory Notes & Guidelines for the period 2007-2012 recognizes that Favourable Reference Populations, - which means the population in a given biogeographical region considered the minimum necessary to ensure the long-term viability of the Species - should be based on the ecology and genetics of the species. The document also suggests that knowledge of the population structure is needed and that “it may be relevant to consider the genetic structure of a species”.Read more:European Commission (2011) Communication from the Commission to the European Parliament, the Council, the Economic and Social Committee and the Committee of the Regions. Our life insurance, our natural capital: an EU Biodiversity Strategy to 2020. Available in: http://ec.europa.eu/environment/nature/biodiversity/comm2006/pdf/2020/1_EN_ACT_part1_v7%5B1%5D.pdfEvans Douglas and Arvela Marita (2011) Assessment and reporting under Article 17 of the Habitats Directive Explanatory Notes & Guidelines for the period 2007-2012. Final Draft prepared for the Habitats Committee.Available in: http://circa.europa.eu/Public/irc/env/habitats/library?l=/habitats_committee/meetings_in_2011/meeting_13_2011/documents/art17_guidelines/_EN_1.0_&a=dCOP 10 Decision X/2.Strategic Plan for Biodiversity 2011-2020.Available in: http://www.cbd.int/decision/cop/?id=12268Laikre Linda, Nilsson Torbjörn, Primmer Craig R., Ryman Nils, and Allendorf Fred W. (2009)Importance of Genetics in the Interpretation of Favourable Conservation Status. Conservation BiologyVolume 23, No. 6, 1378–1381.
  • To sum up, we have the ambitious goals and we also have methods that can be applied. Conservation genetics has produced quantitative methods, tools that can be used to measure genetic diversity – a key factor of viable populations. Furthermore, the current research of conservation genetics has produced information that is available to evaluate the viability of populations in the changing conditions, the chances of species surviving in the future. In other words, the research has already produced applicaple methods which can be used firstly, to clarify the definition of conservation status and secondly, to produce accurate data for monitoring the conservation status of species as well as for supporting sustainable, effective managing decisions in biodiversity policy. To achieve the goals of the Convention on Biological Diversity (CBD), the Aichi Biodiversity Targets and the EU biodiversity strategy to 2020 – is still perhaps possible.
  • I will now move on to introduce genetic diversity in detail.
  • The genome contains the genetic code of an individual. For the most part, the genome consists of a molecule called DNA. The gene sequences code for the specific characteristics of the individual. Therefore, we can say that the gene sequences are a kind of blueprint for how the organism is put together. These sequences differ slightly between different individuals and this is what we refer to as genetic diversity.
  • Gene sequences differ between individuals, even between members of the same family or population. These differences can contribute to differences in how tall individuals are, what colour their fur is, or what kind of temperatures the individual tolerates. When we see a lot of differences, we talk about high genetic diversity. In the photos, we see different colour forms or colour polymorphism in tawny owls (Strix aluco).
  • To summarize, genetic differences can be seen between individuals in the same population.This elk is a little bit different from this other one living near it. Genetic variation can also be observed between different populations. Often the differences between individuals from different populations are greater than between individuals from the same population, so individuals from different populations are more different from each other, which is symbolised by the different colours used here. And on an even greater scale, individuals of different species show even larger genetic differences.
  • In the next slides, I will introduce how genetic diversity is beneficial for populations and how low genetic diversity can affect species.
  • There are populations with very little genetic diversity, such as this one where the elks are given the same colour to represent a very similar genetic background. These populations run the risk of inbreeding depression. Inbreeding depression occurs when genetically similar individuals mate and their offspring get two copies of a ‘bad’ gene. As a result, they have lower fitness or they are less healthy. In most cases, inbreeding happenswhen related individuals mate. It should be noted, however, that in a small population like this, the genetic variation might be so low that even individuals who are not directly related carry the same bad gene variants.
  • In view of this, it is worrying that many endangered species currently suffer from lower genetic diversity. As habitat destruction and global change cause populations to become smaller, genetic diversity also decreases, and inbreeding can become a problem. Actually, a recent study found that 80% of endangered species have lower genetic diversity.Read more: Spielman Derek, Brook Barry W., Frankham Richard (2004) Most species are not driven to extinction beforegenetic factors impact them. PNAS vol. 101 no. 42.
  • Genetic variation can also reflect that populations are well adapted to their local conditions. When two populations of the same species differ genetically, it might mean that the two populations have different gene variants that suit their different environments. Recognizing and maintaining thisvariation isimportant in order to maintain the populations and halt the genetic erosion of species – as mentioned in the Aichi Biodiversity Targets Strategic Goal C.
  • Low genetic diversity is also a problem that will be faced in the future, because genetic variation can help populations adapt to new conditions. Currently, climate change is forcing species to adapt to new conditions, or else move away. Higher genetic diversity means there are more genetic alternatives that might be suited to the new conditions. In a way, possessing higher genetic diversity provides a population with more 'tickets in the lottery’ so that by chance, one of the gene variants will be suited to the new conditions.
  • To summarise, we can say that genetic diversity creates biodiversity. Individuals differ in their genes and these differences can be seen as differences in traits such as height or fur colour. These differences mean that some individuals might be well suited to the changed conditions in the same area or to the conditions in a new area. Populations can adapt to environmental changes, but only if there is genetic variation.
  • We will now move on to case studies and practical examples.
  • In the following, I will introduce: 1) how conservation genetics can be applied in determining where individuals come from and what population or species they belong to , 2) finding out if populations mix in nature, 3) detecting hybrid individuals, 4) checking whether populations are suffering from low genetic diversity, 5)identifying distinct populations and relevant conservation units, 6) predicting the genetic outcome of management or harvesting decisions and finally, 7) checking whether populations are diverse enough to be prepared for the future.
  • Firstly, we can determine where individuals come from and what species they belong to. For example, if we observe an individual elk in nature, we can use genetic methods to determine whether it is more likely to come from the local population, or whether it is an immigrant from another population. This is done by applying genetic markers that can be used on blood samples, hair samples, tissue samples, and so on. By sampling the focus individual and some individuals from the relevant population, we can get the genetic profile of the individual and compare it to the two populations. In this case, it appears that the individuals genetic profile does match the local population, marked here with blue. This is a simple example how genetic data can be used to find out where individuals come from and assigning them to populations. This method can also be used to find out migration routes of animals.
  • Moreover, conservation genetics can determine what species our food belongs to. Here we have an example of how to distinguish endangered tuna species. Several tuna species are widely traded, including the Atlantic bluefin tuna (ABFT; Thunnus thynnus), Pacific bluefin tuna (PFBT, Thunnus orientalis), Southern bluefin tuna (SBT, Thunnus maccoyii), bigeye tuna, (BET, Thunnus obesus), yellowfin tuna (YFT, Thunnus albacares), and albacore (ALB, Thunnus alalunga). Atlantic bluefin tuna is also one of the most endangered trade fish in the world. When the endangered species are prepared and traded as commercial commodities, their identification is often impossible.Read more: Viñas Jordi and Tudela Sergi (2009) A Validated Methodology for Genetic Identification of Tuna Species (GenusThunnus). PLoS One.; 4(10): e7606.
  • Identifying tuna species from tissue samples has been challenging. However, using the combination of two genetic markers, all eight tuna species can be distinguished from any kind of processed tissue. This new DNA tool can improve conservation efforts and trade control.The same kinds of methods, for example DNA barcoding, can be used to identify species. In that case, genetic profile of an individual is compared to genetic information about a species, which can often be found in the literature or in the future, in DNA barcode reference libraries. These methods can also be used when identifying species in an area: are there new species that might have been recently introduced? Read more: Viñas Jordi and Tudela Sergi (2009) A Validated Methodology for Genetic Identification of Tuna Species (GenusThunnus). PLoS One.; 4(10): e7606.
  • By comparing populations genetically, it is also possible to determine whether the populations are mixing in nature. That is, are individuals mating across the populations. When analysing a network of populations, you can genotype them all with the same markers and then compare their genetic profile. If they are very genetically different, most likely individuals are not mating across populations. For instance,it may be desirable that populations of rare species mix because it reduces the risk of inbreeding. Therefore, nature reserves are planned to keep populations connected to each other. With genetic methods, we can check whether they, in fact, are connected, or have been connected in the past (e.g. before a highway was built).
  • I will now further introduce this method with an example study from Spain, the Cantabrian bears.The two Cantabrian subpopulations are remnants of a once large and widespread population of bears in the Iberian peninsula. Cantabrian bears started to decline about 300 years ago.Low population sizes (estimated in 50-60 and 20, for western and eastern subpopulations, respectively) and recent isolation has resulted in low genetic diversity and differentiated allele frequencies. This probably does not reflect what the situation would be without human-induced fragmentation.Populations have been monitored for the last few years through the genetic identification of faeces and hairs. 143 samples could be characterized that corresponded to 76 individuals.Read more:Perez T, Naves J, Vazquez JF, et al. (2010) Evidence for improved connectivity between Cantabrian brown bear subpopulations. Ursus21, 104-108.Pérez T, Vázquez F, Naves J, et al. (2009) Non-invasive genetic study of the endangered Cantabrian brown bear ( Ursus arctos ). Conservation Genetics10, 291-301.
  • One individual was tracked in the eastern population in May 2006 and was subsequently localized three times on his way to the western subpopulation where he was finally recorded in November 2006In addition, three individuals sampled in the eastern subpopulation were genetically assigned to the western subpopulations, being thus identified as migrants.Finally, two individuals sampled in 2008 near the western border of the eastern sub-population were identified as hybrids. Subsequent paternity and maternity analyses could identify a western male and an eastern female as the father and mother of these two individuals. All these results provide evidence for the recent demographic and genetic connection of two recently isolated subpopulations, despite unfavourable habitat (mining and ski resort) and possible barriers (high-speed railway and motorways). Population size increase and habitat improvement might be responsible for this reconnection: the male that was observed to migrate from the eastern to western subpopulation transited an area that is becoming naturally reforestedRead more:Perez T, Naves J, Vazquez JF, et al. (2010) Evidence for improved connectivity between Cantabrian brown bear subpopulations. Ursus21, 104-108.Pérez T, Vázquez F, Naves J, et al. (2009) Non-invasive genetic study of the endangered Cantabrian brown bear ( Ursus arctos ). Conservation Genetics10, 291-301.
  • Sometimes, you can find individuals that have genetic characteristics of two species or two distantly related populations of the same species, that is, hybrids. Hybridization can lead to genetic mixing or “genetic pollution” of the native species, and many management programs try to avoid this process. For example in Finland, there was interest to use captive populations for re-introductions of the endangered lesser white-fronted goose. Read more: Ruokonen et al. (2007) Using historical captive stocks in conservation. The case of the lesser white-fronted goose. Conservation Genetics, Vol. 8. No. 1, pp. 197-207.
  • However, genetic analyses of captive populations showed signals of hybridisation with two other goose species. Therefore, it was recomended that individuals from other wild populations would be a better source for wild stock supplementation instead.Read more: Ruokonen et al. (2007) Using historical captive stocks in conservation. The case of the lesser white-fronted goose. Conservation Genetics, Vol. 8. No. 1, pp. 197-207.
  • Conservation genetics can also monitor populations to check whether they are suffering from low genetic diversity, in other words, if they have experiencedgenetic erosion. This can be done for instance by using genetic markers. If populations have been sampled over a longer timescale, it is also possible to compare past and present levels of genetic diversity. Using calculations, the measure of genetic diversity can be used to estimate population size, and to identify trends in the population size. With this information, breeding programs can be planned to avoid inbreeding or species mixing.
  • This example of Swedish adders demonstrates how the addition of new genetic material from a nearby population saved a population suffering from inbreeding depression. The population has been isolated from other adders for at least a century. Abound 35 years ago the population declined dramatically and has since suffered from severe inbreeding depression. Deformed or stillborn offspring and very low genetic variability has been observed. 20 adult male adders from large and genetically variable populations were released into thispopulation. They remained there for four mating seasons, then the eight surviving snakes were captured and released back into their natal populations. Theadder population that was already close to extinction, has remained ’healthy’ since then! Introducing new genes from a different population enabled the adders to make a dramatic recovery. This result encouraged genetic approaches to conservation and supports the importance of preserving genetic variability as a way of increasing the viability of wild populations.Read more: Madsen et al. (1999) Restoration of an inbred adder population. Nature 402, pp. 34–35.
  • It should be noted, however, that as the risks of low genetic diversity and inbreeding are rather well known, there is also an another side to populations with unique genetic profiles. As mentioned before, populations that have adapted to their local environment may have distinct genetic patterns. These populations may, indeed, be natural gene banks that are important for conservation. This phenomenon will be further introduced in the next slides.
  • Conservation genetics can identify populations that show distinct genetic patterns and therefore recognizeunique parts of biodiversity, or natural gene banks, within species. If you have only one of these “red” populations, which possesses a unique genetic profile and you lose it, you lose a great deal. This kind of genetic structure should be taken into account especially when planning management units.
  • Distinct populations and their management can be further explained by study of salmons in northern Finland and Norway. The Teno river harbours one of the largest salmon populations in the world. Like most salmon rivers, it has been managed as a single ‘management unit’ and decisions about fishing quotas are based on the overall stock size. However, genetic research showed that there are a number of clearly separate populations in different sections of the river.Read more: Vähä, J.-P. K., Erkinaro, J., Niemelä, E., Primmer, C.R. (2007) Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Molecular Ecology 16: 2638-2654Vähä J.-P.K., Erkinaro J., Niemelä E. and Primmer C.R. (2008) Retrospective genetic monitoring of Atlantic salmon populations within a river system over two decades – implications for management. Evolutionary Applications 1: 137-154.
  • This means there is an opportunity to ‘fine tune’ management strategies and fishing regulations so they are optimal for each river section.Further research has also suggested that these genetic differences may occur because individuals have adapted to the specific conditions they experience in a particular river section. Read more: Vähä, J.-P. K., Erkinaro, J., Niemelä, E., Primmer, C.R. (2007) Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Molecular Ecology 16: 2638-2654Vähä J.-P.K., Erkinaro J., Niemelä E. and Primmer C.R. (2008) Retrospective genetic monitoring of Atlantic salmon populations within a river system over two decades – implications for management. Evolutionary Applications 1: 137-154.
  • Genetic methods can also be used to improve conservation measures even though the resources are limited. In the next example, we will introduce effective conservation plan of an endemic plant.Borderea pyrenaica (Dioscoreaceae) is an endemic plant of the Pyrenees. Its range is restricted to a narrow geographic area of about 160 km2 in the Central Pyrenees and pre-Pyrenees. Most of its populations are located in Spain, where large populations cover wide expanses, whereas in France only 12 populations are known. Because of the narrow occurrence France, the plant is considered vulnerable by the International Union for the Conservation of Nature.Read more: Segarra-Moragues, J. G. and Catala´n, P. (2010) The fewer and the better: prioritization of populations for conservation under limited resources, a genetic study with Borderea pyrenaica (Dioscoreaceae) in the Pyrenean National Park. Genetica 138:363–376.
  • Precautionary policy for critically endangeredtaxa encourages the protection and of theentire range of the species. However, vulnerable taxa often have many populationsand individuals and therefore this level of protection is usuallyeither non-existent or limited. Generally, not all populations can protected, so they have to be selected and prioritised for conservation purposes in an objectivemanner. In spite of the narrow range of B. Pyrenaica in France, there is not enough human or economical resources for complete management. Genetic methods were used to identify Relevant Units for its Conservation.Read more: Segarra-Moragues, J. G. and Catala´n, P. (2010) The fewer and the better: prioritization of populations for conservation under limited resources, a genetic study with Borderea pyrenaica (Dioscoreaceae) in the Pyrenean National Park. Genetica 138:363–376.
  • Genetic analysis suggest that five populations would adequately represent the variation of B. Pyrenaica and would allow the preservation of 98.21% of its alleles present in France. Following these recommendations the proposed conservation strategy should minimize costs. This strategy should also guarantee the maintenance of genetic variation that can endow enough evolutionary potential for appropriately collected ex situ stocks and to in situ managed populations. Furthermore, this conservation genetic approach could also be applied to other low-extinction risk categories of subalpine plants. Read more: Segarra-Moragues, J. G. and Catala´n, P. (2010) The fewer and the better: prioritization of populations for conservation under limited resources, a genetic study with Borderea pyrenaica (Dioscoreaceae) in the Pyrenean National Park. Genetica 138:363–376.
  • Genetic information can, furthermore, be used to assess the effect that management actions will have on the species. For example, you might be interested in stocking individuals, that is, supplying populations with new individuals. If you supply this “red” population with genes from the blue population, you will end up swamping the population with non-native genes. On the other hand, it is important to know which populations could be hunted without it affecting the genetic future of the species. In this case, it would be wiser to hunt the blue elk. Naturally, the decisions depend on ecological and economical factors as well, but genetics can play a part in advising the decisions.
  • The next case study introduces how genetic information can be used to make sustainable reintroduction plans.The golden eagle (Aquila chrysaetos) was once widely distributed in the uplands of the British Isles, but is now extinct in Ireland and largely confined to the highlands and islands of Scotland. The decline probably resulted from a combination of human population expansion in rural areas, habitat alterations and persecution. However, the precise extent and severity of the population crash are unclear. Because golden eagles were extinct from Ireland in the early twentieth century, a reintroductionproject was initiated in 2001 that assumed birds from the British population represented the closest genetically related donor stock, thus fulfilling one of the key IUCN criteria for reintroduction. For further management, and given the continued threat to the golden eagle in the British Isles, it is also important to understand how the genetic variability of the population was affected by the decline.Bourke Brian P., Frantz Alain C. Lavers Christopher P., Davison Angus, Dawson Deborah A., Burke Terry A. (2010) Genetic signatures of population change in the British golden eagle (Aquila chrysaetos). Conservation Genetics 11:1837–1846.
  • Genetic methods were used to investigate how the population responded to the decline it experienced in the late nineteenth and early twentieth century.When the current and historical genetic diversity of the eagles was compared, the results showed that the extant population has lost relatively little of its genetic diversity since the nineteenth century. There was evidence for an ancient genetic bottleneck, possibly caused by the fragmentation of a large mainland European population and/or the founding effects of colonising the British Isles. However, genetic analysis suggests that the bottleneck was not severe enough to lead to a substantial reduction in the genetic diversity of the golden eagle in the British Isles.Finally, no evidence for population genetic structure was found. Therefore, all eagles belong to single and coherent population.Read more: Bourke Brian P., Frantz Alain C. , Lavers Christopher P., Davison Angus, Dawson Deborah A., Burke Terry A. (2010) Genetic signatures of population change in the British goldeneagle (Aquila chrysaetos) Conservation Genetics 11:1837–1846
  • For management purposes, the golden eagles of the British Isles should be considered a single population unit. The extinct Irish population was not differentiated from the British one.The results also confirm that individuals from the British population are suitable for the Irish reintroduction efforts.The main objective of conservation measures should, therefore, be to increase population sizes by continuous safeguarding of individuals and habitat management.Read more: Bourke Brian P., Frantz Alain C. , Lavers Christopher P., Davison Angus, Dawson Deborah A., Burke Terry A. (2010) Genetic signatures of population change in the British goldeneagle (Aquila chrysaetos) Conservation Genetics 11:1837–1846.
  • Using conservation genetics, it is also possible to monitor whether populations are diverse enough to be prepared for the future. Genetic diversity gives species a higher chance of possessing gene variants that might be beneficial in the future.
  • The following study of seagrass communities will describe how genetic diversity can promote ecosystem resiliance – the ability of species and communities to resist damage or recover from disturbance.Seagrasses provide habitat for numerous fishes and invertebrates and playan important role in nutrient cycling and sediment stabilization. Zostera marina is a widely distributed, cosmopolitan seagrass that typically dominates seagrass meadows worldwide.Read more:Reusch, Thorsten B. H., Ehlers Anneli,Hämmerli, August and Worm, Boris (2005) Ecosystem recovery after climatic extremes enhanced by genotypic diversity. PNAS, U S A. February 22; 102(8).Procaccini, Gabriele Olsen, Jeanine L. b, Reusch, Thorsten B.H. (2007) Contribution of genetics and genomics to seagrass biology and conservation Journal of Experimental Marine Biology and Ecology 350 234–259.
  • Climate change is characterized by increasing mean temperature and increasing climate variability such as heat waves, storms, and floods. How populations and communities cope with such climatic extremes is a question central to biodiversity conservation.In 2003, an extreme heat wave hit the southwestern Baltic Sea destroying parts of seagrass meadows. In a manipulative field experiment, genetic diversity was found to enhance the recovery of the Zostera maritima communities after the heat wave. Furhermore, the benthic fauna was also found to favour geneticly diverse seagrass meadows. The Zostera maritima patches that were most diverse, harboured more individuals offilter feeders, like juvenile bivalves (Mytilus edulis, Mya truncata, and Cerastoderma edule), grazers, including snails (Rissoa membranacea, Rissoa inconspicua, Hydrobia stagnorum, Bittium reticulatum, and Littorina saxatilis) and isopods (Idotea baltica and Idotea chelipes) than the less diverse patches. Read more:Reusch, Thorsten B. H., Ehlers Anneli,Hämmerli, August and Worm, Boris (2005) Ecosystem recovery after climatic extremes enhanced by genotypic diversity. PNAS, U S A. February 22; 102(8).
  • This field study showed that the biodiversity of seagrass meadows is not reflected in species richness, but in genetic diversity of the key species. Genetic diversity may also act as a buffer against extreme climatic events. Therefore, it is important to maintain both genetic and species diversity to enhance ecosystem resilience and maintain ecosystem services in a world of increasing uncertainty.The diversity that exist within species, population diversity, has been described as the portfolio effect. Like the stability of financial portfolios, population diversity maintains and stabilizes ecosystem services and secures the economies depending on them. Research has demonstrated that the loss of population diversity will, indeed, erode the reliability of ecosystem services faster than species loss alone. Read more:Reusch, Thorsten B. H., Ehlers Anneli,Hämmerli, August and Worm, Boris (2005) Ecosystem recovery after climatic extremes enhanced by genotypic diversity. PNAS, U S A. February 22; 102(8).Procaccini, Gabriele Olsen, Jeanine L. , Reusch, Thorsten B.H. (2007) Contribution of genetics and genomics to seagrass biology and conservation. Journal of Experimental Marine Biology and Ecology 350 234–259.Schindler DanielE., Hilborn Ray, Chasco Brandon, Boatright Christopher P., Quinn Thomas P., Rogers,Lauren A. & WebsterMichael S. (2010) Population diversity and the portfolio effect in an exploited species. Nature 465, 609–612.
  • To sum up, some practical considerations on conservation genetics. It is quite easy to obtain DNA for genetic analysis. Often a single hair or feather will do. It is possible to sample from nesting sites and even faeces without invasive procedures for the animals. The costs of conservation genetics can vary a lot and will depend on the type of study. Species identification of an individual can be cheap, assuming that the species’ genetics is known from before. The more markers are needed, the more expensive the study is. And if you want to know the genetic diversity of the whole population, then you have to sample a fair number of individuals, and that makes it more expensive.It is not necessary to invest in equipment and training to do the genetic work yourself, the work can be outsourced to companies. Furthermore, it’s possible to collaborate with research universities etc.It’s worth pointing out that the most important thing is to define a study question that is well planned and feasible. Conservation genetics cannot give answers to all questions, so it is worthwhile to plan well before doing genetic studies. There are conservation geneticists around Europe that are willing to help also with the planning phases.
  • ConGRESS (Conservation Genetic Resources for Effective Species Survival) is an EU consortium dedicated to transferring current knowledge in conservation genetics and in the analysis of genetic variation data to management professionals and policy makers. ConGRESS is funded by the Seventh Framework Programme (FP7) of EuropeanCommission.
  • ConGRESS genetics

    1. 1. www.congressgenetics.eu
    2. 2. Conservation genetics– a tool for species survival1. Conservation Genetics in biodiversity policy2. Genetic resources What is genetic diversity? High and low diversity3. For effective species survival Practical applications and studies
    3. 3. ConservationGenetics in biodiversitypolicy
    4. 4. Genetic diversity – politicallyimportant• Genetic diversity is recognised as a key component of biodiversity • Biological diversity is comprised of genetic differences within species, the diversity of species and the variety of ecosystems (The Convention on Biological Diversity, CBD) • Three levels of biodiversity: • Genetic diversity: between individuals and populations • Species diversity • Ecosystem diversity
    5. 5. Genetics in legislation• Until recently, genetics has been inadequately represented in European biodiversity policy• The Habitats Directive, the corner stone of Europe’s nature conservation policy, does not directly refer to genetic differences within species • Article 1i defines the Favourable Conservation Status of species in broad terms: • … it is maintaining itself on a long-term basis as a viable component of its habitats, the natural range is not being reduced and there is a sufficiently large habitat to maintain its populations on a long-term basis• In the USA, the Endangered Species Act defines species to include subspecies and distinct population segments
    6. 6. Why is genetics important foreffective conservation of species? • Can the challenges of the biodiversity strategies be met? • Can the conservation status of species be improved? • Can the viability of populations in their natural range in a long-term basis be ensured?Conservation genetics research indicates • Genetic diversity is important for both the short- and long-term viability and future evolution of populations • Genetic diversity is a buffer against population crashes in environmental changes• The Habitats Directive stresses the necessity of research in order to implement meaningful species conservation measures Laikre et al., 2009, Conservation Biology
    7. 7. Genetic diversity: an emergingaspect in biodiversity policy• The UN Strategic Plan for Biodiversity 2011–2020 requires strategies for minimizing genetic erosion and safeguarding genetic diversity (Aichi Biodiversity Targets, Strategic Goal C)• The EU biodiversity strategy to 2020 recognizes that the innovation potential of genetic diversity in ecosystem restoration is largely untapped• Article 17 of the Habitats Directive requires Member States to report about the progress made with the implementation of the Habitats Directive – the present reporting period ends in 2012 • Explanatory Notes & Guidelines for the period 2007-2012 recognizes that Favourable Reference Populations should be based on the ecology and genetics of the species Laikre et al., 2009, Conservation Biology
    8. 8. Future prospects?Conservation genetics offers• Highly applicable tools for measuring genetic diversity• Information to evaluate the viability of populations in the changing conditions• New methods for assessing favourable conservation status provided by the Habitats Directive• Help striving towards the goals of the Convention on Biological Diversity (CBD), the Aichi Biodiversity Targets and the EU biodiversity strategy to 2020
    9. 9. Genetic resourcesWhat is genetic diversity?
    10. 10. What is genetic diversity?• The genome contains the genetic code of an individual • DNA in most species • An individual’s blueprint is encoded in genes. The gene information is encoded by ‘building blocks’: A, C, G, T • The code of a gene varies slightly between individuals  this is genetic diversity Lynx family in Heinburg, Germany. Photos: Joachim S. Müller
    11. 11. Differences create diversity • There are often small differences in the code of a gene, even between individuals of the same population • These genetic differences contribute to individual differences in e.g. height, fur colour, temperature tolerance • More differences = more genetic diversity in individuals, populations and species Tawny owls (Strix aluco) with different plumage colour. Photo: Dick Forsman
    12. 12. Genetic diversity is everywhereGenetic diversity exists • Between individuals • Between populations • Between species
    13. 13. Genetic resourcesHigh and lowdiversity
    14. 14. High genetic diversity helpspopulations survive• Low genetic diversity can lead to inbreeding depression • Genetically similar individuals have a higher risk of producing offspring that have hereditary diseases
    15. 15. Endangered species suffer from lowgenetic diversity• Human induced changes have led to smaller population sizes • Habitat fragmentation caused by urbanisation, forestry, agriculture, fishing etc. • Lower genetic diversity and higher risk of inbreeding• 80 % of endangered species have lower genetic diversity (Spielman et al. 2004, PNAS) Clear-cut in southern Finland. Photo: Marjatta Sihvonen
    16. 16. Genetic diversity can reflectadaptation• Populations that have adapted to their local environment are expected to have distinct genetic patterns• Maintaining these differences can help to maintain the populations and halt genetic erosion Otters. Photo: Cyril Blazy
    17. 17. Genes for the future • Climate change is forcing species to adapt to new conditions or move away • High genetic diversity means there are more genetic variants that might be suited to the new conditions • Higher genetic diversity provides a population with more ‘tickets in the lottery’Dryas octopetala in the Alps, Italy. Photos: Sarah Gregg and Fabio Marini
    18. 18. Creating biodiversity Differences in genes (genetic variation) Differences in an individual’s characteristics Adaptation to changing conditions Locally adapted populations
    19. 19. For effective species survivalStudies and applications
    20. 20. What can conservation genetics doto help preserve diversity?• Where do individuals come from and what population or species they belong to?• Do populations mix in nature?• How to detect hybrid individuals?• Are populations suffering from low genetic diversity?• How to identify distinct populations and relevant conservation units?• How to predict the genetic outcome of management or harvesting decisions?• Are populations diverse enough for the future?
    21. 21. Where do individuals come from andwhat population or species theybelong to? X 
    22. 22. Genetics for forensics – saving Case studyendangered tuna species• The genus Thunnus comprised of eight species known as tunas• Several species widely traded including the Atlantic bluefin tuna (Thunnus thynnus)• One of the most endangered trade fish in the world• Traded as commercial commodities, the identification of endangered species is difficultViñas et al., 2009, PLoS One
    23. 23. DNA cannot be hidden Case studyin tuna salad• DNA-based methodologies provide very precise tools for identifying marine species• Using genetic markers, all eight tuna species can now be distinguished from any kind of processed tissue• This new DNA tool can improve conservation efforts and trade controlViñas et al., 2009, PLoS One
    24. 24. Do populations mix in nature?• If populations are genetically different, most likely they do not mix = no gene flow• Check whether populations are connected Photo: Mick Melvin
    25. 25. Assessing past and recent Case studyconnectivity• Bears in the Cantabrian mountains (Spain) are critically endangered (D) in the IUCN Red List• Formerly one large, but now two small, subpopulations separated by 30-50 kilometres• Recent isolation of these subpopulations can be seen as differences in their genetic profiles Perez et al, Ursus 2010 Photo: José Mª F. Díaz-Formentí Perez et al., Conservation Genetics 2009
    26. 26. CaseGenetic methods identified: study• Natural reforestation of intervening habitat has resulted in recent migration from the eastern to the western subpopulations• Two cubs as a result of ‘between-population’ matings• Gene flow, as would have occurred naturally in historical times, has been achieved! Perez et al, Ursus 2010 Perez et al., Conservation Genetics 2009 Photo: Bob Jagendorf
    27. 27. CaseDetecting hybrid individuals study• Hybrids: Individuals that have genetic characteristics of two species• Lesser white-fronted goose (Anser erythropus) listed as vulnerable on the IUCN Red List• Has suffered a rapid population reduction in key breeding populations in Russia, decline predicted to continue• The Fennoscandian population has undergone a severe historical decline, and has not yet recovered Lesser white-fronted goose that escaped from captivity in Espoo, Finland. Photo: Matti Rekilä
    28. 28. Captive population unsuitable for Case studythe wild• Genetic signals of hybridisation with two other goose species in captive population • Unsuitable for wild stock supplementation • Supplementation with other individuals from other wild populations recommended instead Ruokonen et al. 2007, Conservation Genetics
    29. 29. Are populations suffering from lowgenetic diversity?Conservation genetics can Monitor genetic diversity • Compare past and present levels Estimate population size • See whether population size is changing Plan breeding programs to avoid inbreeding or species mixing
    30. 30. Genetic rescue Case study• A population of Swedish adders suffered from inbreeding depression • Stillborn offspring, low genetic variability• Researchers released 20 males from a nearby population → breeding success and population size increased• Recovery corresponded to increase in genetic diversity Adder in spring mood. Madsen et al. 1999, Nature Photo: Marjatta Sihvonen
    31. 31. Gene banks within species
    32. 32. Identifying distinct populations• Genetically distinct populations can be valuable to protect• Conservation genetics can • Find distinct genetic patterns • Identify priority populations for conservation • Plan units for conservation or management Management Management unit 1 unit 2
    33. 33. Discovering distinct Case studygenetic patterns• Teno river salmon in northern Finland and Norway - one of the largest salmon populations in the world• Previously considered as one management unit • Conservation genetics researchers showed there were many distinct genetic units within the river Vähä et al. 2007, Molecular Ecology Vähä et al. 2008, Evolutionary Applications
    34. 34. CaseWhat do the differences mean? study• Changes in management strategies are being made to recognise and protect the distinct population units within the river • When deciding catch limits• Results suggest that individuals may be adapted to the specific conditions of each river section • Ecological information also suggests this Teno salmon. Photo: Panu Orell Vähä et al. 2007, Molecular Ecology Vähä et al. 2008, Evolutionary Applications
    35. 35. Prioritizing populations for Case studyconservation• Borderea pyrenaica is an endemic plant of the Pyrenees• Classified as vulnerable in the IUCN Red List• Only 12 populations in France Borderea pyrenaica in the French Pyrenees Photo: Marc Leclercq Segarra-Moragues, J. G. and Catala´n, P. 2010, Genetica
    36. 36. CaseThe problem of vulnerable species study• The high relative abundance of vulnerable species often precludes management of all populations and individuals• Vulnerable species require a cost-effective management plan • In France, genetic information was used to identify relevant conservation units in order to make a successful management plan for B. Pyrenaica Segarra-Moragues, J. G. and Catala´n, P. 2010, Genetica
    37. 37. Relevant Conservation Units of Case studyB. Pyrenaica• With limited human and economical resources, all 12 populations of B. Pyrenaica in France cannot be protected• Genetic analyses support differentiation of the B. Pyrenaica populations into different management units• Five populations would allow preservation of over 98 % of the genetic variation of B. Pyrenaica• This approach could potentially be applied to other low- extinction risk category species Segarra-Moragues, J. G. and Catala´n, P. 2010, Genetica
    38. 38. Predicting the genetic outcome ofmanagement or harvesting decisions?• Which individuals/ populations should be used for stocking?• Which individuals/ populations can be hunted? Hunting OK No stocking
    39. 39. Golden eagles in the British Isles – Case studyone or two populations?• Golden eagle (Aquila chrysaetos)• Once widely distributed in the British Isles• Now extinct in Ireland, mainly found in the highlands of Scotland• Can the British population be used to reintroduce eagles in Ireland? Golden eagle at the bird of prey centre in Hagley. Photo: Alex Hay Bourke et al. 2010, Conservation Genetics
    40. 40. Past and present diversity Case studycompared by genetic methods• Genetic diversity of the modern British population was compared to British and Irish museum specimens • Only slight evidence for a loss of genetic variation • The population persisted despite ancient bottleneck• No evidence for population genetic structure • Therefore, all eagles belong to the same population Bourke et al. 2010, Conservation Genetics
    41. 41. Safeguarding one population and Case studyhabitat• The golden eagles of the British Isles should be considered a single population unit – the extinct Irish population was not differentiated from the British one • Individuals from the British population are suitable for the Irish reintroduction effort• The main objective of conservation measures: • Increasing population sizes by safeguarding of individuals • Habitat management Bourke et al. 2010, Conservation Genetics
    42. 42. Are populations diverse enough tosurvive in the future?
    43. 43. Seagrasses: genetic diversity and Case study survival in the changing world? • Seagrasses are an ecologically successful group of marine angiosperms • Seagrasses provide habitat for fishes and invertebrates and play an important role in nutrient cycling and sediment stabilization • i.e. help to maintain ecosystem services in a changing world • Zostera marina is the key species of seagrass meadows worldwideSeagrass medow in the Baltic Sea. Reusch et al. 2005, PNAS,Photo: Metsähallitus 2008 Procaccini et al. 2007, J. Exp. Mar. Biol. Ecol.
    44. 44. CasePromoting ecosystem resilience study• In 2003, an extreme heat wave hit the south-western Baltic Sea • Seagrass communities with higher genetic diversity recovered faster from the heat wave • Genetic diversity promoted ecosystem resilience!• The benthic fauna also preferred genetically diverse seagrass meadows • More genetic diversity in seagrass  more individuals of bivalves, snails and isopods Reusch et al. 2005, PNAS, Procaccini et al. 2007, J. Exp.Mar. Biol. Ecol.
    45. 45. Biodiversity in genes Case study– preparing for the future• Genetic diversity of key species can replace the role of species diversity in a species-poor coastal ecosystem• High genetic diversity can provide a buffer against extreme climatic events• Genetic diversity is important for maintaining both genetic and species diversity in order to enhance ecosystem resilience Reusch et al. 2005, PNAS, Procaccini et al. 2007, J. Exp.Mar. Biol. Ecol.
    46. 46. Practical considerations• DNA for genetic analysis is easy to obtain • Single hair, feather, scale or leaf• Costs: • 10 to 50 € per individual • 500 to 25 000 € per study • The overall price depends on methods and numbers of populations• Genetic work can be outsourced• Choosing the right tools is important • Contact conservation geneticists when planning the project • Advice available about samples and analyses needed to answer the questions you are interested in More information: www.congressgenetics.eu
    47. 47. More information: www.congressgenetics.eu
    48. 48. Copyright issues• The photographs in this presentation are used under creative commons license or permission by the photographer and should not be used for other purposes.• More information: • Joachim S. Müller • Dick Forsman • Cyril Blazy • Sarah Gregg • Fabio Marini • Mick Melvin • José Mª F. Díaz-Formentí • Bob Jagendorf • Marc Leclercq • Alex Hay

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