Northern Bottlenose Whale Genomics

Procurement Hub – Fredericton

301 Bishop Drive

Fredericton, NB E3C 2M6

22 July 2019

F5211-190273

ADVANCED CONTRACT AWARD NOTICE

TITLE: Northern Bottlenose Whale Genomics

ACAN:

The purpose of this Advance Contract Award Notice (ACAN) is to signal the government’s intention to award a contract for these services to Dalhousie University, 1355 Oxford St, Halifax, NS B3H 4R2. Before awarding a contract, however, the government would like to provide other suppliers with the opportunity to demonstrate that they are capable of satisfying the requirements set out in this Notice, by submitting a statement of capabilities during the ACAN posting period.

If other potential suppliers submit a statement of capabilities during this ACAN posting period that meets the requirements set out in the ACAN, the government will proceed to a full tendering process on either GETS or through traditional means, in order to award the contract.

If no other supplier submits, on or before the closing date, a statement of capabilities meeting the requirements set out in the ACAN, a contract will be awarded to the pre-selected supplier.

INTRODUCTION:

Fisheries and Oceans Canada (DFO) requires the services for low-depth genome resequencing for northern bottlenose whale.

BACKGROUND:

The northern bottlenose whale (Scotian Shelf population) is listed as Endangered under the federal Species at Risk Act (SARA). Fisheries and Oceans Canada (DFO) has prepared a recovery strategy and an action plan for the population.

OBJECTIVES:

The Marine Gene Probe Lab (MGPL) will prepare biopsy tissue samples for sequencing including DNA extraction, purification, quantification, and quality control for required sequencing standards. DNA from at least 20 individuals will be individually barcoded and prepared for sequencing using Illumina NexteraXT Library Preparation Kits, and sequenced on an Illumina NovaSeq instrument. DNA libraries will be standardized for a target sequencing depth of 10X.

WORK REQUIREMENT:

Evaluate the performance of proposed methods for identifying genome-wide polymorphisms, summarise curated SNP dataset, assess range-wide and regional diversity metrics, compose an unrooted phylogenetic tree. Alignment and linkage based methods for identifying the sex of individuals from resequencing data will be evaluated and compared to morphology-based criteria for sex identification. Diversity metrics and a haplotype network of incidentally sequenced mitogenomes. A workplan outlining the next steps required for a comprehensive analysis of population structure (Phase II).

PHASE 2 (proposed) – Provide analyses of population structure using genomic data. We will use established (Principle Components Analyses, fastSTRUCTURE) and emerging (individual clustering using SNMF, machine-learning clustering using t-SNE) methods of identifying population genetic subdivision. Characterizing fine-scale population genetic structure in northern bottlenose whale has been limited by the low diversity and limited number of targeted markers from a few regions of the genome, and because a genome-wide SNP dataset considers all genomic positions it will be able to more definitively address whether genetic structure is, or is not, present between samples from different geographic regions. Study would be presented at conferences and submitted for peer reviewed publication.

PHASE 3 (proposed) – Analyses of genomic regions under selection and reconstruction of historical demography. The deep dives of northern bottlenose whale during foraging are likely to impose strong selective pressures. We will search for regions of the genome under selection by comparing rates of synonymous and non-synonymous substitutions across all samples, identifying regions that may be under selection. The Gully MPA is genetically distinct from more northern populations of northern bottlenose whale, and as the most southern population may be subject to adaptive challenges not encountered elsewhere in the range of northern bottlenose whale, such as temperature and anthropogenic activities. We will test whether genomic regions could be under divergent selection between the Gully MPA and other populations by analyzing genetic differentiation across the northern bottlenose whale genome. The effect of climatic fluctuations prior to the last glacial maximum on the historical demography of northern bottlenose whale is currently unknown, and we will reconstruct the evolutionary history of northern bottlenose whale using PSMC. Study would be presented at conferences and submitted for peer reviewed publication.

TASKS AND DELIVERABLES:

The Contractor must deliver a report including a summary of methods, evaluation of performance for identifying genome-wide polymorphisms, a curated SNP dataset for all individuals, initial consideration of range-wide and regional diversity metrics, an unrooted phylogenetic tree, and an outline of next steps. Alignment and linkage based methods for identifying the sex of individuals from resequencing data will be evaluated and compared to morphology-based criteria for sex identification. Diversity metrics and a haplotype network of incidentally sequenced mitogenomes will be included.

MANDATORY CRITERIA:

The Contractor must have access to biopsy samples from the Scotian Shelf of northern bottlenose whales .

ESTIMATED VALUE

The total value of the contract shall not exceed $27,300 excluding all applicable taxes for the firm period from contract award to 27 March 2020. Each subsequent Optional Phase is estimated at $9,400 (each) which will happen within the firm period.

SECURITY REQUIREMENT

No Security Requirement

TRADE AGREEMENTS APPLICABILITY OR OTHER OBLIGATIONS:

No Trade Agreements apply.

GOVERNMENT CONTRACTS REGULATIONS EXCEPTION AND LIMITED TENDERING REASONS:

The following policy requirements are applicable to this ACAN process:

Applicable Exceptions to Soliciting Bids under the Government Contracting Regulations (GCRs) (Section 6):

Section 10.2.1 Section 6 (d) only one person or firm is capable of performing the work applies to this ACAN for the following reasons:

There are no known alternative sources of supply. It is feasible and affordable to compete the requirement.

CONTRACT PERIOD:

The period of the contract is from contract award to 27 March 2020 inclusive.

SUPPLIER’S RIGHT TO SUBMIT A STATEMENT OF CAPABILITIES:

Suppliers who consider themselves fully qualified and available to provide the services described herein, must submit a Statement of Capabilities in writing to the Contracting Officer identified in this Notice on or before closing date. The Statement of Capabilities must clearly demonstrate how the supplier meets the advertised requirements.

CLOSING DATE FOR SUBMITTING STATEMENT OF CAPABILITIES:

6 August 2019 at 2:00 p.m. (ADT)

Inquiries and statements of capabilities are to be directed to:

Michael Peters

Senior Contracting Officer – Contracting Services

Procurement Hub – Fredericton

Telephone: (506) 429-2359

Email: DFOtenders-soumissionsMPO@dfo-mpo.gc.ca