Title: Lamprey ecology & genetics Phd project code




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NHRP Project Proposal


Title: Lamprey ecology & genetics PhD

Project code: QU13-01

pFACT: 12198

NHRP student:

A.N. Other (to be advertised)

NHRP Manager:

Dr Neil Reid

NHRP Project Manager:

Emma Dorman

NHRP Client Officer(s):

Tony Waterman

QUB academic supervisor(s):

Dr Chris Harrod (1st)

Prof Paulo Prodöhl (2nd)

Dr Neil Reid (3rd)


Project Outline (100 words max):

This 3 year studentship aims to assess the distribution and abundance of sea, brook and river lamprey in Northern Ireland whilst resolving the taxonomic and phylogenetic difficulties in differentiating the brook and river lamprey. Trophic ecology approaches including Stable Isotope Analysis will be used to determine the ecology of the river lamprey.



What question(s) may be answered by this project?

  1. What is the current conservation status of lamprey in NI including distribution and abundance?




  1. Are brook and river lamprey separate species?




  1. Are river lamprey in NI entirely non-anadromous?




  1. What are the impacts of physical barriers to lamprey migration?




To which of the NHRP research theme(s) does this project apply?

i) NIEA statutory duties



  • Species distribution, abundance and habitat requirements

ii) Biodiversity in the wider countryside



  • Northern Ireland Priority Species

  • Ecological genetics




To which NIEA policy driver(s) does this project apply?

EU Habitats Directive Bern Convention

Convention of Biological Diversity NI Irish hare Species Action Plan

All-Ireland Species Action Plan Northern Ireland Priority Species List Irish Red Data Book






Type (Please tick):

Full project 

Short Contract 

Studentship 

Other 

Starting date: 01/07/2013

End date: 15/09/2016

Duration: 3.2 years

Background:
There are three species of lampreys (Agnatha or jawless fish) in Ireland belonging to two genera found throughout Europe and the British Isles; the sea lamprey (Petromyzon marinus), the river lamprey (Lampetra fluviatilis) and the brook lamprey (Lampetra planeri).
The river lamprey is primarily an anadromous species that spawns in accessible rivers, but feeds as adults in coastal waters and estuaries. However, some non-migratory populations have been reported that do not make the migration to coastal habitats but migrate downriver into lakes to feed, for example at Loch Lomond in Scotland as well as in some lakes in Finland and Russia (Maitland 2003). Recently, freshwater feeding in a non-anadromous population of river lampreys has been reported from the largest lake in the British Isles, Lough Neagh (Goodwin et al. 2006; Inger et al. 2010). The brook lamprey is a purely freshwater species occurring in streams and lakes. River and brook lamprey populations are generally in decline across Europe and are currently protected under the European Union Habitats Directive, Annexes IIa and Va, Appendix III of the Bern Convention and as a ‘Long List Species’ in the UK Biodiversity Action Plan. The sea lamprey is listed as ‘near threatened’ on the current Irish Red List (King et al. 2011). Consequently, Special Areas of Conservation (SACs) have been established for these species.
Whilst the basics of their distribution and abundance (Goodwin et al. 2009) and ecology (Goodwin et al. 2006; Goodwin et al. 2008; Inger et al. 2010) are roughly known in Ireland this information is now out-of-date and not relevant as a basis for Conservation Assessments under the Habitats Directive during the current reporting period (2013-2019).
More generally, relatively little is still known regarding population and evolutionary genetics of lampreys; most notably the brook and river species. Lampreys are among the most primitive freshwater species in the British Isles. Like other endemic freshwater fish species (e.g. brown trout, arctic charr, coregonids, sticklebacks), their evolutionary history is closely associated with the retreat of the ice following the last ice age. Thus, current day populations are most likely derived from several genetically distinct lineages of anadromous forms that reached newly formed rivers and Loughs. Change from anadromous forms to freshwater (e.g. resident river lamprey and/or brook lamprey) in Britain and Ireland has occurred more or less independently in each river system within the past 18,000 years. It is most likely that, adaptive and non-adaptive changes have taken place among populations within and among water catchments. Indeed, this has been clearly demonstrated for other anadromous fish species (e.g. sea trout vs. brown trout) where substantial genetic heterogeneity among populations within and among water systems has been observed. Similar genetic differences are expected to occur in lampreys. Furthermore, in parallel to what has been observed in salmonid species, it is likely that freshwater lampreys have arisen, in some river systems, from lineages that colonized at different times, post-glacially giving rise to sympatric reproductively isolated populations.
This anadromous origin has important implications for the study/conservation of Lampetra species. In particular, it means that it is not possible to generalize on the relationship between these forms, as freshwater types could have evolved independently in each catchment under distinct environmental pressures. Thus, what may apply in one catchment may not be the case in others.


For instance, one current hypothesis is that river and brook lampreys may represent a ‘paired species’, where river lampreys continue the ancestral anadromous migration to estuarine or marine habitats to feed, whilst brook lampreys represent a recent evolutionary adaptation and are non-parasitic. These arguments have obvious implications for the identification of meaningful conservation units including the designation of appropriate SACs for these species.



Objectives and Methods:

  1. Determine the current distribution and abundance of sea, brook and river lamprey in NI [NIEA Priority]

Two techniques will be used; i) an electrofishing survey of ammocoetes and ii) a trapping survey of adults. The distribution of survey sites will depend on existing information. Water Management Unit (WMU), Rivers Agency (RI) and the Agri-Food and Biosciences Institute (AFBI) conduct electrofishing for salmonids and kick-sample monitoring at regular stations which contribute incidental data on the abundance of lamprey in riffle (not the ideal habitat) or their presence/absence at kick-sampling sites. Ideally, we will select sites that do not occur within the same 10km squares as existing monitoring sites so that at the end of the PhD all sources of data can be combined so as not to duplicate records but fill in as many 10km squares as possible. Moreover, we would want this survey to have a reasonably uniform distribution of survey effort, for example, each 20km square (n=36). Sea lamprey ammocoetes can be easily distinguished from brook and river lamprey ammocoetes but the latter cannot be distinguished. See genetics objective below. Estimates of density (fish.m-2) and total abundance will be estimated.





  1. Verify the taxonomic status of brook and river lamprey using molecular genetics techniques [NIEA Priority]

The phenotype of adult brook and river lamprey caught during trapping will be recorded using morphology (length, weight, eye diameter and mouth shape), taxonomic approaches (oocyte counts) and molecular analysis (using mitochondrial DNA sequencing). Genetic analysis will be used to determine whether brook and river lamprey are discrete species or genetically indistinguishable morphs of the same species. If they prove to be discrete species that can be distinguished the successful molecular markers will be used to analyse tissue samples taken from the ammocoetes collected during the electrofishing survey so that there distribution can be accurately mapped.





  1. Determine the phylogenetic history of brook and river lamprey [NIEA Priority]

A comparative phylogeographical analysis of brook and river lamprey will be carried out using both mitochondrial (mtDNA) and nuclear sequencing data. It is anticipated that additional nuclear markers from putative coding regions will also be available for screening. This will become available from ongoing whole genome shotgun sequencing for both species currently being developed as part of parallel ongoing project within the supervisor research group. This will necessitate sourcing additional samples from elsewhere in Ireland, the Great Britain and Europe for comparison.







  1. Population structure and trophic ecology of river and brook lamprey.

Assessment of levels of genetic variation and the degree of population structuring of both brook and river lamprey within Lough Neagh will be carried out using both available microsatellites and mtDNA markers. Sample processing and screening will be carried out with the help of a Robotic DNA workstation and an ABl96 capillary system. Data analyses will be carried out using modem statistical genetic approaches in particular those based on Coalescent Genealogical Samplers. In parallel to genetic analysis, as part of the same study variation in morphology and life-history characteristics (mass-length relationships, size at metamorphosis, fecundity) of both brook and river lamprey will be compared. Using a trophic ecological approach (see below), the possible driving mechanisms leading to feeding preferences will be examined (molecular approaches will used to define these differences). Samples from other geographical areas will be used for comparison. An examination will be carried out to determine whether all river lamprey populations in Lough Neigh are exclusively freshwater feeding, or are there some, which are anadromous. If anadromous lampreys are found, the relative contribution of each migratory component will be determined. Comparisons with genetic data will be carried out. Sexing of adult lampreys will be carried out in order to assess population sex ratios. Furthermore, a comparative study on the fecundity and gonad development between anadromous and non-anadromous populations.





  1. Assessment of lamprey trophic ecology.

Inger et al. (2010) used stable isotopes to characterise seasonal differences in the diet-of freshwater feeding river lampreys in Lough Neagh. This will be developed further through analysis of carbon(δC), nitrogen (δN) and sulphur (δS) stable isotopes to identify the migration and feeding history origin of adult lampreys due to the large isotopic differences between fresh, brackish and marine habiats (Harrod et al. 2005; Adams et al. 2008; Inger et al. 2010). Stable isotopes will also be utilised to quantify and compare the trophic ecology of river and brook lamprey ammocoetes. Genetics methods (mtDNA 12S rDNA marker) will be used to confirm adult trophic ecology. Analysis of data will be carried out using a range of statistical approaches (e.g. isotope mixing models, univariate and bivariate approaches)




  1. Determine the impact that physical barriers have on fish movements and/or population structure [NIEA Priority]

Pairs of sites will be selected for survey during electrofishing and trapping with one above and one below a potential barrier to movement (e.g. weir). Species occurrence and abundance will be compared above and below such barriers to infer their potential impact on sea verses brook/river lamprey (where the former are believed to be impeded by barriers whilst the latter appear less affected). Genetic sampling might also reveal population structure between- and within- rivers that may also highlight the impact of barriers to movement. It might also be desirable to conduct some fish tracking work using radio-tags or pingers to track lamprey migration.



NB: These are indicative research chapters only. Developments may inform the degree of investment of time and resources in any one theme. The final PhD thesis will have a minimum of 5 research chapters; thus not all ideas may come to fruition within the lifetime of the project. Should there be any shortfall we will endeavour to obtain MSc students to make up the missing components but this cannot be guaranteed.



Outcomes:

  1. Brief monthly update on progress presented to the Project Board

  2. Quarterly report on progress

  3. Annual report once every 12 months

  4. Final thesis submitted by 15/09/2016




Timeframe:




Year 1

Year 2

Year 3

Year 4

Tasks

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W

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Literature review











































Electrofishing & trapping











































Molecular development











































Stable Isotope Analysis











































Taxonomy











































Phylogeography











































Population structure











































Manuscript writing











































PhD submission














































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