Rethinking the Stock Concept: A Phylogeographic Approach

Abstract

The “stock” is the fundamental population unit of legally mandated conservation efforts, yet its formal definition in the scientific literature and in two U.S. conservation acts is varied and so general that attempts to apply it in practice are arbitrary. Because choice of stocks deserving management protection is sometimes politically contentious, improvement of the working definition is important. A key element should be the degree to which a population can be considered an evolutionarily significant unit. We propose that a hierarchial classification scheme be applied to stock designations. Category I populations, having the highest probability of being evolutionarily significant units, are characterized by a discontinuous genetic divergence pattern where locally adapted and closely related genome assemblages are separated from others geographically and by significant genetic distances. Category II populations are similarly characterized by significant genetic diversity, but with weak geographic partitioning. Category III populations are the converse of II, having little genetic differentiation between assemblages that are clearly separate and likely to be reproductively isolated. Category IV assemblages have the lowest probability of being evolutionarily significant units and are characterized by extensive gene flow and no subdivision by extrinsic barriers. In addition to phylogeographic designation, the following information is used in the classification, as indicated by single‐letter abbreviations: distribution (a), population response (b), phenotypic (c), and genotypic (d) information. Included are evidence both for and against designating population as a separate stock. In the designation “Type II a/bc,” for example, information to the right of the solidus would be evidence for “lumping,” to the left would be for “splitting.” Missing letter abbreviations would signify lack of reliable data. Note that phylogeographic designation depends on the results of selection operating to produce a locally adapted genome (indicated by differences in demographic, phenotypic, and genotypic measures) and on gene flow (indicated by differences in distribution or by movement data). Hierarchial stock categorization allows resource managers to direct limited resources to the populations most deserving of protection, that is, the populations that are most likely to be evolutionarily significant units. Using this comprehensive classification of stock allows preliminary, conservative splitting of assemblages where data are lacking without the danger that these divisions will become entrenched as biological dogma.

The “Evolutionarily Significant Unit” concept and its applicability in biological conservation

“…Definitions by some other authors (Waples 1991;Dizon et al 1992;Vogler & Desalle 1994;Bowen 1998) tend to overlap with subspecies concepts. Some recent works, taking into account the ever-increasing availability of genetic data, have suggested, or sometimes even tended to force, the adoption of criteria exclusively based on molecular phylogenies, while largely ignoring all other otherwise measurable adaptive components (Avise 1994;Moritz 1994a,b Yuan et al 2011) rather than ESUs.…”

“…On the other hand, an ESU lineage might comprise single/multiple populations, as well as groups exchanging a degree of gene flow such as meta-populations, this being always dependent on specific life histories (Fraser & Bernatchez 2001). Similarly to the "species" concept, several, sometimes contrasting, definitions have been proposed for ESU in the course of time (Ryder 1986;Waples 1991;Dizon et al 1992;Moritz 1994a,b;Vogler & Desalle 1994;Fraser & Bernatchez 2001;de Guia & Saitoh 2007). All of these definitions, however, aim at defining an identical "entity", i.e.…”

“…Definitions of ESU concept Ryder (1986) Population units presenting significant adaptive variation based on concordance between sets of data derived by different techniques (life history information, morphometric, range and distribution data, and genetic data) Definitions stressing the importance of molecular data Dizon et al (1992) Populations exhibiting discontinuous genetic divergence patterns, geographic isolation and significant genetic distances Avise (1994) Sets of populations derived from consistently congruent gene phylogenies Moritz (1994a,b) Populations that: (1) are reciprocally monophyletic for mtDNA alleles and (2) demonstrate significant divergence of allele frequencies at nuclear loci Bowen (1998) Populations which show evidence of long-term isolation Fraser and Bernatchez (2001) A lineage demonstrating highly restricted gene flow from other such lineages within the higher organizational level of the species Definitions stressing the importance of using molecular analysis and ecological data Vogler and Desalle (1994) Groups that are diagnosed by characters which cluster individuals or populations to the exclusion of other such clusters Waples (1991) A population or group of populations that: (1) is substantially reproductively isolated from other conspecific population units; (2) represents an important component of the evolutionary legacy of the species Crandall et al (2000) Prefer identification of distinct populations characterized by genetic and ecological inexchangeabilities over recent and historical times De Guia and Saitoh (2007) Full ESUs can be defined solely when information about both neutral genetic variation and adaptive variation is available; otherwise the taxa are ascribed to partial ESU judgements on how distinctive a population should be, before it becomes eligible for being recognised as an ESU, were based on ecological as well as on variously measurable genetic information, thereby trying to take into account its effective evolutionary distinctness (see definitions by Ryder 1986 but also Crandall et al 2000 in Table I). Definitions by some other authors (Waples 1991;Dizon et al 1992;Vogler & Desalle 1994;Bowen 1998) tend to overlap with subspecies concepts.…”

“…Despite the fact that molecular approaches clearly represent a breakthrough in the rapid assessment of many imperfectly known taxa, sometimes occurring in insufficientlyexplored areas, or for the discovery of cryptic biodiversity, a variety of sources, including ecological, behavioural, bio-geographic and morphological data, are equally valid for a strictly scientific assessment of conservation units. Of course, an important prerequisite for the use of non-genetic data consists in the assumption that observed traits are based on inheritable attributes, so that they can provide objective hierarchical information (Avise 1989;Waples 1991;Dizon et al 1992;Moritz 1994a,b;Vogler & Desalle 1994;Lai & Pullin 2004). Convergence of information between molecular and non-molecular data may often provide clear evidence for ESU identification, but what conclusions can be drawn in those cases where information remains controversial or perhaps insufficient?…”

Distribution Patterns of Five Mammals in the Jomon Period, Middle Edo Period, and the Present, in the Japanese Archipelago

“…The ESU concept was initiated to provide a basis for prioritizing taxa for conservation efforts with the goal of protecting the evolutionary heritage and potential within a species. The criteria for defining ESU's are not uniformly established (Moritz 1994); however, most researchers agree that classification as an ESU should include phylogenetic distinctiveness of alleles across multiple independent loci (Avise and Ball 1990;Dizon et al 1992;Moritz 1994). The second type of information that can be obtained from intraspecific analyses is the description of genetic structure, or gene flow patterns, between populations that have not evolved independently.…”