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Developing a"Genetic Scorecard": A World-first for Scotland

Scotland’s Biodiversity Progress to 2020 Aichi Targets

The following case study summarises a SEFARI Think Tank involving the Royal Botanic Gardens Edinburgh and Scottish Natural Heritage. SEFARI Think Tanks are designed to address challenging and often contested research questions of national and international importance. This project brought together experts to address Aichi Target 13 on the conservation of genetic diversity. The project has established a world-first method to help understand and conserve genetic diversity in some of Scotland's most iconic wild species. This fills a significant gap in addressing this international target, as the practical tool will enable other countries to assess its genetic diversity and compare what has been measured in Scotland.


Work Completed


The nature crisis is being recognised as a major global challenge equal to and interlinked with climate change. Nature is deteriorating at an unprecedented rate: three-quarters of the land-based environment and two-thirds of marine environments have been significantly altered by human activities; while one-eighth of animal and plant species are threatened by extinction.  

The UK Government have signed up to several international conventions relating to the conservation of nature. One of the most significant of these is the Convention on Biological Diversity (CBD). The CBD is concerned with the conservation of all the living organisms and, at a meeting in 2010 in Nagoya, Japan, they established a Strategic Plan for 2011-2020 with twenty global Aichi targets. In signing the convention, the UK, and Scotland, have agreed to translate the Strategic Plan and the Aichi targets into national and local level strategies and plans - in Scotland, this is covered by the Biodiversity Route Map to 2020

Aichi Target thirteen (T13) focuses on the conservation of genetic diversity. Genetic diversity is a generic term for differences within species because of variations in their DNA.

This term covers genetic variability (the number and characteristics of different types of organisms) distinctiveness (the degree to which an organism is different and distinct from others). This latter trait includes ‘evolutionary divergence’ (e.g. lineages that have been isolated for long periods of time and hence have become genetically distinct).

Genetic diversity is essential for all species to thrive and to adapt to changing environments. Against a backdrop of climate change, habitat alteration, anthropogenic movement and elevated disease transmission, species lacking genetic diversity will be less able to respond, adapt and survive.

“AICHI Target 13: By 2020, the genetic diversity of cultivated plants and farmed and domesticated animals and of wild relatives, including other socio-economically as well as culturally valuable species, is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.”


The wording of T13 places a strong emphasis on the conservation of genetic diversity in cultivated plants and domesticated animals, compared to wild species. Although some attention is directed towards ‘wild relatives’ and ‘socio-economically’ and ‘culturally valuable species’, the species description largely omits wild species that comprise the vast majority of genetic diversity on the planet. While appropriate conservation of genetic diversity within those species emphasised in T13 is certainly important, we argue that the target should be expanded significantly and refocused on the conservation of genetic diversity in wild species, living in natural populations.

In Scotland, and the UK more widely, there are well-established approaches for assessing genetic diversity in species of agricultural importance (e.g. rare livestock breeds, crop wild relatives), and a methodology has been established for ornamental plants. For forestry, the approach to conserving genetic resources is at an earlier stage of development in the UK, but an outline national strategy has now been developed. However, there is no clear strategy to deal with the category of ‘other species of socio-economic importance’ in Scotland, the UK or elsewhere. What species are deemed socio-economically and culturally important? How can the genetic diversity of these species be assessed to allow comparisons? A SEFARI Gateway Think Tank was created to bring together expertise to look at an approach for addressing Target 13.


There is a lack of information on how to identify species of socio-economic and/or cultural value (i.e. wild species) in Scotland and no clear approach for assessing Target 13 once they have been identified. To address this issue we adopted two key steps. First, we established a process for defining and selecting wild species to include. Second, we developed a T13 genetic scorecard approach that is flexible enough to cope with many different issues whilst having sufficient coherence to enable comparative reporting. 

1. Defining species for inclusion

There is no agreed national list of species of wild species for Scotland. Generating such a list involves making subjective decisions. Cultural valuation is subjective and will depend on who you ask. Likewise, the outcomes of economic valuations are methodology dependent, and even where an agreed method is available, robust valuations are simply not available for many species.  

Given these challenges, we adopted a pragmatic approach to selecting a subset of species to focus on. We identified a set of categories reflecting the reasons why a species might be considered socio-economically or culturally important: 

  • Conservation value
  • Cultural importance
  • Species provide evironmental benifits 
  • Commercial value
  • Species collected for food or medicine

The below table shows the resulting 25 species of socio-economic or cultural value and what category they fall into (orange).




Selection Criteria

Conservation target

Culturally important

Ecosystem Services

Food/ Medicines


Common bent (Agrostis capillaris)






Atlantic salmon (Salmo salar)






Blaeberry (Vaccinium myrtillus)






Bramble (Rubus fruticosus)







(Cantharellus cibarius)






Elderberry (Sambucus nigra)






Freshwater pearl mussel

(Margaritifera margaritifera)






Golden eagle 

(Aquila chrysaetos)






Great Yellow Bumblebee 

(Bombus distinguendus)






Hazel gloves (Hypocreopsis rhododendri)







(Campanula rotundifolia)






Yorkshire fog 

(Holcus lanatus)







(Calluna vulgaris)





Purple moor-grass 

(Molinia caerulea)






Oak (Quercus spp)






Raspberry (Rubus idaeus)






Red deer (Cervus elaphus)






Red grouse 

(Lagopus lagopus)






Red squirrel 

(Sciurus vulgaris)






Roe deer 

(Capreolus capreolus)






Scots pine 

(Pinus sylvestris)






Scottish wildcat 

(Felis silvestris grampia)






Sea trout/brown trout 

(Salmo trutta)






Papillose bog-moss 

(Sphagnum papillosum)






Woolly Willow

(Salix lanata)







2. The Genetic Scorecard

Next, we developed a genetic scorecard that is flexible enough that can be used in different countries. Factors that vary among countries include:

  • Costs: The capacity of a given country to report on T13 will depend on the resources available, the level of knowledge of a given biota, and the diversity and scale of the country in question. A key requirement of an effective system for reporting on Target 13 is scalability and applicability in situations where resource availability is limited.
  • Geographical scales of data holdings: Where spatial data are used for reporting on Target 13, a practical issue relates to the scale at which data are held. Additional steps may be required to up-scale or down-scale reporting where different datasets are held and curated at different levels (e.g. state vs. national levels). This is a particular issue for the UK where considering priority species for Scotland requires either steps to extract Scotland specific data from UK-wide compilations or consideration of issues at a UK scale for Scottish priority species. The following table provides an example of this genetic scorecard being used to assess the Scots Pine.



Scientific name

Pinus sylvestris

Common Name

Scots pine

UK IUCN Category

LC (global status)

T13 Status



Hermaphrodite, wind-pollinated, widely distributed tree. Present in 84 natural stands, often small and fragmented. Natural stands represent only 10% of trees in Scotland. Genetic marker studies show that it retains large amounts of neutral genetic diversity. Some evidence of adaptive differentiation in Scotland on a west-east axis (Salmela, 2011) (Donnelly et al. 2018).

Current threats

Plant pathogens represent the major emerging threat (Dothistroma septosporum races introduced on Corsican and lodgepole pine) (Piotrowska et al., 2018).

Contribution of the Scottish population to total species diversity

Molecular evidence for putative separate lineage in northwestern Scotland, although nuclear markers indicate very low differentiation, even from continental Europe (Ennos et al., 1997). Scotland does, however, contain a uniquely oceanic adapted population (Ennos et al., 1997) (Donnelly et al. 2018).

Diversity loss: population declines 

Multiple small populations with no regeneration coupled with a biased age-structure (towards older trees) compromises the sustainability of many populations. However, there is limited risk of imminent genetic diversity loss due to high levels of standing variation in adult trees (assuming no catastrophic population losses due to pathogens). 

Diversity loss: functional variation 

The general persistence of the species across its range in Scotland is not threatened, which minimises likely loss of adaptive variation. There are risks to loss of high elevation populations across its range which may lead to some loss of adaptive variation.  

Diversity loss: divergent lineages

Limited divergence from European populations precludes loss of major divergent lineages. The most genetically distinct populations are in the northwest of Scotland around Shieldaig. These populations are not currently threatened. 


Limited risk to loss of genetic integrity to native Scots pine stands from exotic stands due to buffer zone around existing stands in which planting of non-local seed is prohibited  

Low turnover / constraints on adaptive opportunities

Deer grazing is a major limitation on turnover and regeneration, but the risk is mitigated in c. 20% of populations where active management in place.

In situ genetic threat level

MODERATE (major limitations to regeneration, in the face of emerging pathogen threats presents a moderate risk of loss of genetic variation) 

Confidence in in-situ threat level

HIGH (assessment based on good demographic data supported by direct data on genetic variation, population differentiation and detailed knowledge of Scots Pine biology)

Ex-situ representation

15 accessions from 14 10 Km squares are held at the Millennium Seed bank. These include representation in all 5 UK ‘standard’ tree seed zones and all 7 ‘Scots pine’ seed zones in which native Scots pine stands occur 


Representation in seed bank collection

Current management interventions

Grazing controls at c 20% of sites promote regeneration providing adaptive opportunities.

Overall T13 status


Overall T13 status explanation

Despite the fragmented nature and small size of many populations, the longevity of individual trees minimises imminent loss of genetic diversity. Management to promote regeneration at 20% of sites supports some ongoing evolutionary processes, and there is a wide representation of all seed zones in seed banks which likely catches the main adaptive variation in Scotland.

Future steps

Grazing pressures ultimately restrict regeneration and opportunities for natural selection and adaptation to introduced pathogens and climate change. The long-term security of Pinus sylvestris genetic variation would benefit from improved grazing management of populations and establishment of dynamic genetic conservation reserves across the native range in Scotland.


Richard Ennos, University of Edinburgh


Stephen Cavers, Centre for Ecology and Hydrology

Peter Hollingsworth, Royal Botanic Garden Edinburgh


For the first time, this poject has developed a clear approach for assessing genetic diversity of wild species for use worldwide. You can read the full report on the Scottish Natural Heritage website here. The project has also produced a range of proposals that will directly contribute to biodiversity strategy development nationally and internationally through interaction with Scottish Working Group on Aichi Target 13 and the IUCN Conservation Genetics Specialist group to the Convention on Biological Diversity (CBD). This work project is particularly timely as 2020 is the last year of this current strategy framework and plan and the international community are negotiating the next one for the post-2020 era. 


Scots Pine in the Cairngorms National Park. Those found in Beinn Eighe are unique and are genetically distinct having adapted to the wetter conditions.

This project has also advanced the understanding of genetic diversity conservation on the ground by contributing to the establishment of the first UK Genetic Conservation Unit (GCU).  Beinn Eighe, in Wester Ross, is habitat to a unique population of Scots Pine that are genetically distinct and unique due to having adapted to the wet conditions there. It is hoped that Beinn Eighe will be the first of many GCU’s to be established across the UK. GCUs are forest areas which contain sufficient numbers of individuals to retain high genetic diversity (ideally 500, but as low as 50 where only scattered individuals are available) and which receive gene flow from other sites. Dynamic gene conservation units are managed to encourage natural regeneration and the action of natural selection so that there is ongoing adaptation to changing environmental conditions. A network of 3,200 dynamic conservation units have been established across Europe, encompassing 4,000 different populations or about 400 species. 

Project Partners

  • Royal Botanic Garden Edinburgh (Project Lead Professor Pete Hollingsworth)
  • Scottish Natural Heritage
  • University of Edinburgh
  • Moredun Research Institute
  • James Hutton Institute
  • University of Sheffield
  • Centre for Ecology and Hydrology
  • Scotland’s Rural College
  • Biomathematics and Statistics Scotland
  • Science and Advice for Scottish Agriculture
  • Royal Botanic Garden Kew
  • Bumblebee Conservation Trust
  • Botanical Society of Britain and Ireland
  • University of Salford
  • University of the Highlands and Islands
  • University of Glasgow
  • University of Aberdeen

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