Catchment-Scale Conservation Units Identified for the Threatened Yarra Pygmy Perch (Nannoperca obscura) in Highly Modified River Systems

Chris J Brauer,Mark Adams,Michael P Hammer,Luciano B Beheregaray,Peter J Unmack

doi:10.1371/journal.pone.0082953

Abstract

Habitat fragmentation caused by human activities alters metapopulation dynamics and decreases biological connectivity through reduced migration and gene flow, leading to lowered levels of population genetic diversity and to local extinctions. The threatened Yarra pygmy perch, Nannoperca obscura, is a poor disperser found in small, isolated populations in wetlands and streams of southeastern Australia. Modifications to natural flow regimes in anthropogenically-impacted river systems have recently reduced the amount of habitat for this species and likely further limited its opportunity to disperse. We employed highly resolving microsatellite DNA markers to assess genetic variation, population structure and the spatial scale that dispersal takes place across the distribution of this freshwater fish and used this information to identify conservation units for management. The levels of genetic variation found for N. obscura are amongst the lowest reported for a fish species (mean heterozygosity of 0.318 and mean allelic richness of 1.92). We identified very strong population genetic structure, nil to little evidence of recent migration among demes and a minimum of 11 units for conservation management, hierarchically nested within four major genetic lineages. A combination of spatial analytical methods revealed hierarchical genetic structure corresponding with catchment boundaries and also demonstrated significant isolation by riverine distance. Our findings have implications for the national recovery plan of this species by demonstrating that N. obscura populations should be managed at a catchment level and highlighting the need to restore habitat and avoid further alteration of the natural hydrology.

Highlights

Human activities such as land development, agriculture, and exploitation of natural resources have long been acknowledged as driving processes behind habitat fragmentation and degradation [1,2]
This can occur when hierarchical structure due to the presence of strong barriers for dispersal creates clusters of populations that are not necessarily better explained by spatial distances between demes. To assess this possibility partial Mantel tests were performed to assess for hierarchical population structure, such as that identified by the analysis of molecular variance (AMOVA) and STRUCTURE
A simple Mantel test was performed for C4, the largest genetic cluster identified within a lineage, in order to test for isolation by distance (IBD) at a local scale

Summary

Introduction

Human activities such as land development, agriculture, and exploitation of natural resources have long been acknowledged as driving processes behind habitat fragmentation and degradation [1,2] This can decrease population connectivity through reduced migration and gene flow, leading to higher genetic differentiation among populations and lowered levels of genetic diversity within [3]. Understanding the spatial scale of patterns of genetic diversity is important for species conservation in order to identify the evolutionary processes shaping these patterns and to detect when populations become demographically and genetically independent [16,17] This information can be used to estimate the geographical extent of conservation units defined by genetic criteria [18,19], such as the popularly used Evolutionarily Significant Units (ESUs) and Management Units (MUs) (see Moritz [20] and Crandall [21] for definitions). These conservation units can inform conservation management strategies by recognising the historical isolation of evolutionary lineages (i.e. ESU), and the functional and demographic independence of populations (i.e. MU) [22]

Methods

Results

Conclusion