. Author manuscript; available in PMC: 2021 Nov 1.

Published in final edited form as: Infect Genet Evol. 2020 Sep 28;85:104570. doi: 10.1016/j.meegid.2020.104570

Table 1:

Evolutionary Ecology Framework

	ECOLOGY	EVOLUTIONARY BIOLOGY	EVOLUTIONARY ECOLOGY

EXAMPLE QUESTIONS	• How does intraspecific diversity contribute to host-vector-pathogen interactions?	• How do pathogens co-evolve with their vectors and hosts?	• How do ecological interactions create selective forces or impact migration rates to cause micro-evolutionary changes?
	• How important are multiple infections in driving disease dynamics?	• By what molecular mechanisms do pathogens replicate and how does that impact pathogen evolution?	• What are the ecological consequences – such as changes in geographic, host or vector range, abundance, or virulence – of these micro-evolutionary changes?
	• How do species interactions explain the distribution and abundance of different species?

ASSUMPTIONS	• Individuals within a species or group considered identical	• Constant/irrelevant population densities (Hartl and Clark 1989)	• Distribution and variance of genetic variation is constant (Holt 2005)
	• No evolutionary change (short timescales)	• Fitness in light of ecological interactions considered as constant
		• Most evolution is neutral

NECESSARY DATA & EXAMPLE APPROACHES	Necessary Data: Measures of diversity (e.g. phenotypes, genotypes, species counts, functional traits); Measures of disease progression and transmission Examples: Devevey et al. 2015¹⁵⁵, Walter et al. 2016¹¹⁷	Necessary Data: Sequencing (e.g. multi-locus markers, whole genome sequencing, reduced representation sequencing) Examples: Brisson et al. 2010¹⁵⁶, Becker et al. 2016¹⁸	Necessary Data: Sequencing (e.g. multi-locus markers, whole genome sequencing, reduced representation sequencing); Measures of diversity (e.g. phenotypes, genotypes, species counts, functional traits); Examples: MacDonald et al. 2019 bioRxiv¹⁵⁷; Becker and Han 2020 bioRxiv¹⁵²