Allis (Alosa alosa) and Twaite (Alosa fallax) shad monitoring data sampled from the rivers Wye, Usk and Tywi, using Mitochondrial DNA techniques (2014)

Populations of allis shad (Alosa alosa Lacépède) and twaite shad (Alosa fallax L.) have declined across their geographic range over the last century. Although both species are widespread around the coast of the British Isles, spawning populations in the UK are now largely restricted to the Rivers Severn, Wye, Usk, and Tywi, which drain into the Bristol Channel. As a result, both species are protected under UK and international legislation.

In response to the need to monitor population status and inform conservation objectives for these species, the former Countryside Council for Wales and Environment Agency Wales, now Natural Resources Wales (NRW), developed a semi-quantitative and cost-effective method for assessing recruitment potential through the collection and analysis of shad eggs. However, this method is unable to distinguish between the two Alosa species, and there is a risk that eggs belonging to other fish species may be incorrectly identified as shad eggs.

The aim of this study was to use genetic techniques to address these limitations by confirming species identification and reducing uncertainty associated with egg-based monitoring.

The specific objectives were to:

Determine whether the collected eggs belonged to Alosa species.

Determine the relative proportions of A. fallax and A. alosa using three genetic markers: mitochondrial DNA (mtDNA), the nuclear marker nif1, and six microsatellite loci.

A total of 226 eggs were successfully genotyped. Of these, 85% were confirmed as belonging to Alosa species, demonstrating a high level of accuracy in field identification by the survey team. The non-Alosa eggs were identified as minnow (Phoxinus phoxinus) and chub (Squalius cephalus).

The results indicate that the extent of putative shad spawning in the River Tywi is slightly less extensive than suggested by the egg survey data alone. However, the upper extent of shad spawning in the River Wye was confirmed as Brynwern Bridge, approximately 9 km upstream of the previously recorded upper limit at Builth Wells.

Identifier: NRW_DS115891

Alternative Title

Metadata Language: English

Lineage: Staff were provided with clear instructions and standardised field equipment, including pre-labelled 1.5 ml Eppendorf tubes containing buffer solution and cool boxes for sample storage and transport.

Up to 20 eggs were collected from each sampling site and preserved in ATL (lysis) buffer within pre-labelled 1.5 ml Eppendorf tubes (Table 1). Eggs were either dispatched immediately to the laboratory using an overnight courier service or refrigerated overnight and dispatched the following day.

During the 2013 spawning season, NRW staff collected 240 individual eggs from 12 sampling sites within the Rivers Tywi, Usk, and Wye using kick-sampling techniques.

Two mitochondrial DNA (mtDNA) haplogroups of the cytochrome b (CytB) gene have previously been identified within Alosa species. Haplogroup A is predominantly associated with A. alosa, while haplogroup F is predominantly associated with A. fallax.

Using the primers described by Alexandrino et al. (2006), a 401 bp fragment of the CytB gene was successfully amplified. Of the 226 eggs extracted, 191 samples were successfully amplified using CytB-specific primers.

Additional Information: Monitoring Allis and Twaite Shad: Quality assurance and species Identification using molecular techniques. Dr E Hardouin, Dr D Andreou and S Stuart Bournemouth University

Dataset Reference Date (Publication): 2015-05-31

Temporal Extent

Begin date: 2013-06-10

End date: 2013-06-13

Topic category

Biota

Owner

Natural Resources Wales (NRW) -

Maes-y-Ffynnon, Penrhosgarnedd, Bangor, Gwynedd, LL57 2DW, Wales

http://naturalresources.wales/?lang=en

Originator

Natural Resources Wales (NRW) -

Maes-y-Ffynnon, Penrhosgarnedd, Bangor, Gwynedd, LL57 2DW, Wales

http://naturalresources.wales/?lang=en

Originator

Bournemouth University -

Bournemouth University, Fern Barrow, Talbot Campus, Poole, Dorset, BH12 5BB, UK

https://www1.bournemouth.ac.uk/

Extent

Geographic Extent: SIR FYNWY - MONMOUTHSHIRE

Geographic Extent: BLAENAU GWENT - BLAENAU GWENT

Geographic Extent: MERTHYR TUDFUL - MERTHYR TYDFIL

Geographic Extent: TOR-FAEN - TORFAEN

Geographic Extent: CASNEWYDD - NEWPORT

Geographic Extent: CAERFFILI - CAERPHILL

Geographic Extent: CAERDYDD - CARDIFF

Geographic Extent: BRO MORGANNWG - THE VALE OF GLAMORGAN

Geographic Extent: PEN-Y-BONT AR OGWR - BRIDGEND

Geographic Extent: CASTELL-NEDD PORT TALBOT - NEATH PORT TALBOT

Geographic Extent: ABERTAWE - SWANSEA

Geographic Extent: SIR GAERFYRDDIN - CARMARTHENSHIRE

Geographic Extent: SIR BENFRO - PEMBROKESHIRE

Geographic Extent: SIR CEREDIGION - CEREDIGION

Geographic Extent: POWYS - POWYS

Map representing the geographic extent of the dataset

Distribution

Format Type and Description

Documents ( Unknown )

Specification

Final report in Microsoft Word and Adobe PDF formats; Electronic field sheets in PDF format
Binary ( Unknown )

Specification

Excel spreadsheet containing RFLP, mtDNA and microsatellite results
Text or Plaintext ( Unknown )

Specification

FASTA sequence files (.fas)

Data quality

Quality Scope: Dataset

Conformity: Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services
Explanation: This dataset has not been assessed for conformance to the referenced INSPIRE regulation.
Degree: false

Lineage: Staff were provided with clear instructions and standardised field equipment, including pre-labelled 1.5 ml Eppendorf tubes containing buffer solution and cool boxes for sample storage and transport.

Up to 20 eggs were collected from each sampling site and preserved in ATL (lysis) buffer within pre-labelled 1.5 ml Eppendorf tubes (Table 1). Eggs were either dispatched immediately to the laboratory using an overnight courier service or refrigerated overnight and dispatched the following day.

During the 2013 spawning season, NRW staff collected 240 individual eggs from 12 sampling sites within the Rivers Tywi, Usk, and Wye using kick-sampling techniques.

Two mitochondrial DNA (mtDNA) haplogroups of the cytochrome b (CytB) gene have previously been identified within Alosa species. Haplogroup A is predominantly associated with A. alosa, while haplogroup F is predominantly associated with A. fallax.

Using the primers described by Alexandrino et al. (2006), a 401 bp fragment of the CytB gene was successfully amplified. Of the 226 eggs extracted, 191 samples were successfully amplified using CytB-specific primers.

Keywords

GEMET - INSPIRE themes, version 1.0

Habitats and biotopes

Type: Theme

Citation

Date (Publication): 2008-06-01

Code: geonetwork.thesaurus.external.theme.httpinspireeceuropaeutheme-theme

Keywords

NRW Thesaurus

River Wye (Afon Gwy)
Shad
biological surveys
biological monitoring
alosa alosa
allis shad
twaite shad
alosa fallax
River Usk

Type: Theme

Citation

Date (Publication): 2026-08-27

Code: geonetwork.thesaurus.local.theme.converted_nrw-keywords

Code: British National Grid (EPSG::27700)

Content Information

NRW Profile

Custom Elements

NRW Related Title: Monitoring allis and twaite shad : quality assurance and species identification using molecular techniques

Constraints

Limitations on Public Access and Use

Restriction type: Other restrictions

Access Constraints Directive

Limitations: no limitations

Access Constraints Text

Other constraints: There are no access restrictions to this data. NRW may release, publish or disseminate it freely.

Use Constraints

Use constraints type: Other restrictions

Other constraints: © CNC/NRW, 2015. There are no use restrictions on this data. Recipients may re-use, reproduce, disseminate this data free of charge in any format or medium, provided they do so accurately, acknowledging both the source and NRW's copyright, and do not use it in a misleading context. It is the recipient's responsibility to ensure the data is fit for the intended purpose, that dissemination or publishing does not result in duplication, and that it is fairly interpreted. Advice on interpretation should be sought where required. To avoid re-using old data, users should periodically obtain the latest version from the original source.

Attribution Statement

Licence

Other constraints: Open Government Licence

Metadata

File Identifier: 4f4c4942-4343-5764-6473-313135383931 XML

Metadata Language: English

Resource type: Dataset

Metadata Date: 2026-10-01T14:43:31.643Z

Metadata Standard Name: NRW

Metadata Standard Version: 1.0

pointOfContact

Data Services Team -

Natural Resources Wales (NRW), Maes y Ffynnon, Penrhosgarnedd, Bangor, Gwynedd, LL57 2DW

http://naturalresourceswales.gov.uk/splash?orig=/

Publishing Body

Access the portal

Full access to the portal and metadata.

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Extent

Extent

Distribution

Distribution

Quality

Data quality

Keywords

Keywords

Citation

Keywords

Citation

Spatial Reference System

Content

Content Information

NRW Profile

Custom Elements

Constraints

Constraints

Limitations on Public Access and Use

Access Constraints Directive

Access Constraints Text

Use Constraints

Attribution Statement

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Metadata

Metadata

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