Molecular genetic and stable isotope signatures reveal complementary patterns of population connectivity in the regionally vulnerable southern pygmy perch (Nannoperca australis)

Abstract

Population connectivity (and isolation) and genetic diversity in declining species are important considerations for species recovery and habitat restoration programs. For lotic species, stream confluences with major rivers may be a determinant of population isolation among streams, although small-scale dynamics in population connectivity within streams may also represent attributes of population functioning (e.g. resilience, recolonisation) that are important for species recovery programs. In this study, we examined the importance of among- and within-stream patterns of population connectivity and genetic diversity in the regionally vulnerable southern pygmy perch (Nannoperca australis) in a series of degraded streams in south east Australia in which population declines have been reported. We used molecular markers (mtDNA and microsatellites) to examine among-stream patterns of population connectivity and genetic diversity, and molecular markers and stable isotopic signatures of nitrogen and carbon to examine within-stream connectivity in the species. Results revealed that populations of N. australis are isolated among streams, and that streams therefore represent functional population units for species recovery and habitat restoration programs. Within-streams, local populations were semi-discrete and connected by various degrees of dispersal, with the degree of connectivity differing between the streams. Genetic bottlenecks were not detected, although the effective population size of N. australis in the more fragmented stream may be lower than in the stream where greater population connectivity was found. Protecting and augmenting refugial habitat of extant populations and restoring corridor functions between refugia within streams will generate the greatest biological response at within-stream scales.

Introduction

Population connectivity (i.e. gene flow and dispersal) determines to a large degree the properties of local populations that may be of importance for the conservation and recovery of declining species (Frankel and Soulé, 1981, Frankham et al., 2002). In particular, population connectivity, and its inverse (i.e. isolation), influences effective population size (Frankel and Soulé, 1981, Frankham et al., 2002), patterns of genetic variation among and within local populations (Wright, 1931, Slatkin, 1985) and the degree of independence of immigration, recruitment and recolonisation processes among them (Brown and Kodric-Brown, 1977, Lowe, 2003). Although many species are naturally isolated across heterogeneous landscapes (Hanski and Gaggiotti, 2004), anthropogenic changes to landscape connectivity have induced further reductions in population connectivity in some species, thereby reducing their distribution and abundance (Pringle, 2001, Edwards et al., 2004, Bank et al., 2006, Scott, 2006). In some cases, population declines have resulted in loss of genetic diversity and inbreeding in formerly outcrossing populations (Hedrick and Kalinowski, 2000, Knaepkens et al., 2004, Frankham, 2005, O’Grady et al., 2006), although in other cases, declining populations have maintained sufficient genetic diversity to persist locally (Sumner et al., 2004, Neville et al., 2007). Thus, the effective conservation of declining species, and restoration of their habitat, requires knowledge of the deterministic factors that isolate populations at various spatial scales, and levels of genetic diversity that are maintained in extant populations (Smallwood, 2001, Frankham et al., 2002, Peakall and Lindenmayer, 2006).

For lotic species, stream confluences may represent extrinsic, long-term determinants of population isolation (Meffe and Vrijenhoek, 1988, Fagan, 2002, Bond and Lake, 2003a, Lowe et al., 2006, Grant et al., 2007), and thus demarcate lotic population units at which to target conservation and habitat restoration measures (Meffe and Vrijenhoek, 1988, Bond and Lake, 2003a). However, small-scale patterns of population connectivity and isolation within streams may also represent attributes of population functioning (i.e. recovery, resilience, genetic rescue) that are of importance for conservation and restoration initiatives (Gowan and Fausch, 1996a, Johnston, 2000, Bond and Lake, 2003a). Thus, for lotic fauna of conservation concern, evaluating the influence of stream structure across landscapes and local factors within streams in shaping patterns of population connectivity and genetic diversity represent important steps for the design of effective conservation and habitat restoration strategies for the species.

Molecular genetic analysis has played a central role in detecting patterns of population structuring in lotic fauna, with traditional measures of gene flow and genetic isolation, such as Wright’s (1931)F_ST, and more recent non-equilibrium assignment methods both contributing information about population connectivity (Manel et al., 2005, Hanfling and Weetman, 2006). Whereas traditional population genetic measures characterise long-term genetic processes at equilibrium (i.e. mutation, gene flow, genetic drift) (Slatkin, 1985), assignment methods characterise more recent dynamics within- and among-local populations, such as the proportion of residents versus migrants and the potential source population of migrants in a focal population (Cournet et al., 1999, Manel et al., 2005). Some recent studies have coupled the use of ecological data with molecular markers to reveal patterns of dispersal and subdivision in natural populations (Berry et al., 2004, Gaggiotti et al., 2004, Wilson et al., 2004), with acquired biogeochemical signatures (e.g. elemental concentration or isotopic signatures) contained in animal tissues or bone proving to be highly complementary tracers of animal movement (Campana and Thorrold, 2001, Clegg et al., 2003, Rubenstein and Hobson, 2004, Miller et al., 2005, Charles et al., 2006). Natural abundance stable isotopic signatures of elements that are acquired via local dietary sources, such as nitrogen and carbon, can be informative over relatively small spatial and temporal scales for lotic species (Cunjak et al., 2005), as studies have shown that the residence time for these elements in animal tissues is in the order of months (Frazer et al., 1997, Maruyama et al., 2001) and that primary sources of the elements in aquatic ecosystems can vary in their isotopic composition over small geographical scales (Peterson and Fry, 1987). Thus, the combined use of molecular markers and natural abundance isotopic signatures of nitrogen and carbon has the potential to be a powerful approach for studying population connectivity in stream fauna.

It was the purpose of this study to examine population connectivity in the southern pygmy perch (Nannopreca australis), and its patterns of genetic diversity, in a series of geomorphically degraded streams in south eastern Australia in which population declines associated with habitat loss have been reported (Bond and Lake, 2005). The among-stream analyses used molecular data (mitochondrial and microsatellite DNA) to evaluate patterns and magnitudes of genetic exchange and diversity at this scale. The within-stream analyses incorporated both molecular data and natural abundance stable isotope signatures of nitrogen and carbon as markers of population structure. If local populations were isolated at within-stream scales, we expected to reveal significant values for measures of genetic differentiation and a high proportion of individuals classified to their capture site on the basis of both molecular and stable isotope data. We expected that the degree of isolation of local populations would be inversely correlated with their levels of genetic diversity, as predicted by conservation genetic theory (Frankel and Soulé, 1981, Frankham et al., 2002), and that reported population declines in N. australis throughout these streams (Bond and Lake, 2005) would be accompanied by recent genetic bottlenecks. Findings are discussed in the context of conservation and habitat restoration strategies for N. australis and other declining species of freshwater fish.