Jane M. Hughes

Dispersal and recruitment in streams: evidence from genetic studies

Analysis of genetic variation among populations of stream invertebrates provides a measure of the consequences of effective dispersal, and can be used to determine the extent of movement within and between streams and to infer the likely mechanisms involved. In our recent studies of rainforest stream invertebrates, we have found considerable genetic differentiation among populations of fully aquatic taxa, indicating limited in-stream movement on a very small scale. Adult flight appears to be the principal mechanism of dispersal for aquatic insects; however, analysis of the genetic structure of larval populations of some species also suggests that in-stream movement is limited to a small spatial scale. Furthermore, detailed analysis of the genetic structure of larval populations suggests that recruitment at the reach scale is the result of only a few adult matings and most likely from oviposition by only a few females. We propose that dispersal capability and the stochastic effects of recruitment are key determinants of observed spatial and temporal variation in community structure in some streams.

Genes in Streams: Using DNA to Understand the Movement of Freshwater Fauna and Their Riverine Habitat

Today, decisions regarding the management and conservation of populations are often informed to some degree by population genetics. A fundamental measure sought by decisionmakers is the degree of connectivity between populations, which, when approached from a genetic perspective, may be influenced by many factors, making it difficult to generalize across taxa, habitats, or life histories. In the case of freshwater-limited fauna, the shared constraint of habitat structure (e.g., a dendritic stream network) imposed on all species in the system simplifies the task. A number of models have been proposed that predict how populations of taxa with different life-history traits and dispersal capabilities interact within structured freshwater habitats of this kind. In this article, we summarize these models and illustrate the general patterns of phylogeographic structure expected to occur under different scenarios of freshwater population connectivity. Additionally, we describe how the genetic structure of stream inhabitants can reflect historical changes in the physical structure of streams and thus open a window on past patterns of connectivity. A greater understanding of these concepts will contribute to an improved multidisciplinary approach to managing freshwater ecosystems.

Small but mighty: headwaters are vital to stream network biodiversity at two levels of organization

Abstract Headwaters (stream orders 1–2) traditionally have been considered depauperate compared to mid-order streams (orders 3–4)—a conclusion that arises from a perception of streams as linear systems and emphasizes change in average &agr; (local) diversity along streams. We hypothesized an opposite pattern for &bgr; (among-site) diversity and suggest that headwaters might account for a large degree of basin-scale biodiversity if considered within the more realistic framework of streams as branching networks. We assembled pre-existing biodiversity data from across the globe to test this hypothesis broadly at the population-genetic (mitochondrial haplotype diversity within species) and community (species/taxonomic diversity) levels, with a focus on macroinvertebrates. We standardized 18 (9 headwater and 9 mid-order) population-genetic and 16 (10 headwater and 6 mid-order) community-level ecoregional data sets from 5 global ecozones for robust comparisons of &bgr;-diversity estimates between the 2 stream-size categories. At the population-genetic level, we applied measures of among-site variation commonly used at both population-genetic (FST and &PHgr;ST) and community (Sørensens dissimilarity with both presence/absence and abundance data) levels and developed a novel strategy to compare expected rates of loss of &ggr; (regional) diversity as individual sites are eliminated sequentially from regions. At the community level, we limited analyses to Sørensens presence/absence measures. We found that Sørensens dissimilarity was significantly greater among headwaters than among mid-order streams at both population-genetic and community levels. We also showed that individual headwater reaches accounted for greater proportions of genetic &ggr; diversity than did mid-order reaches. However, neither FST nor &PHgr;ST was significantly different between stream-size categories. These measures, which have been used traditionally for comparisons of population-genetic variation, measure proportions of total variation rather than solely among-site variation (i.e., they also are influenced by within-site variation). In contrast, Sørensens dissimilarity measures only among-site variation and, therefore, is presumably more useful for reflecting general &bgr; diversity. Overall results suggest that, on average, headwaters probably contribute disproportionately to biodiversity at the network scale. This finding demands a shift in thinking about the biodiversity contributions of small headwaters and has strong conservation implications for imperiled headwater streams around the world.

When oceans meet: a teleost shows secondary intergradation at an Indian–Pacific interface

The Indo–West Pacific is characterized by extraordinary marine species diversity. The evolutionary mechanisms responsible for generating this diversity remain puzzling, but are often linked to Pleistocene sea level fluctuations. The impact of these sea level changes on the population genetic architecture of the estuarine fish Lates calcarifer are investigated via a natural experiment in a region of the Indo–West Pacific known to have undergone considerable change during the Pleistocene. L. calcarifer, a coastline–restricted catadromous teleost, provides an excellent model for studying the effects of sea level change as its habitat requirements potentially make it sensitive to the regions physical history. Evidence was found for a large phylogenetic break (4% mtDNA control region; 0.47% ATPase 6 and 8) either side of the Torres Strait, which separates the Western Pacifc and Indian Oceans, although some mixing of the clades was evident. This suggests clinal secondary introgression of the clades via contemporary gene flow. Further, populations on Australias east coast appear to have passed through a bottleneck. This was linked to the historical drying of the Great Barrier Reef coastal lagoon, which resulted in a significant loss of habitat and forced retreat into isolated refugia. These results suggest that historical eustatic changes have left a significant imprint on the molecular diversity within marine species as well as among those in the Indo–West Pacifc.

Phylogeography of the freshwater fish, Mogurnda adspersa, in streams of northeastern Queensland, Australia: evidence for altered drainage patterns

A phylogeographic survey was used to elucidate the relative roles of historical processes and contemporary gene flow in structuring the genetic pattern observed with Mogurnda adspersa. This species of freshwater fish is found in the rivers and streams of the northeastern highlands of Queensland, Australia. Specifically, this project focused on populations in the Tully and Herbert Rivers in the Atherton Tablelands. Sequence analysis indicated that three distinct clades exist in the headwaters of the Tully River. The population sampled from one of the Tully River streams (Cheetah Creek) contained haplotypes that displayed ≈ 3.4% sequence divergence from other haplotypes detected in this river. Furthermore, these haplotypes formed part of the clade which exists throughout not only the Herbert River but other surrounding drainages in the area. These results support the hypothesis that the current genetic structure is strongly affected by changes in drainage patterns due to geomorphological processes that occurred in the recent past.

Gene Flow among Conspecific Populations of Baetis sp. (Ephemeroptera): Adult Flight and Larval Drift

The genetic structure of populations of Baetis sp. (Ephemeroptera:Baetidae) was used to draw inferences about the means of dispersal within and between stream systems of the Conondale Range, Queensland, Australia. Allozyme electrophoresis was used to examine allelic frequencies at five variable loci in geographically distant populations of nymphs in the same drainage and in nearby populations in different drainages. The results showed widespread gene flow between drainages and a tendency for local differentiation. We concluded that adult flight represents an effective means for dispersal between drainage systems. The differentiation between populations at a local scale and erratic deviations from Hardy Weinberg equilibrium could have occurred if the nymphs collected from any stream were the offspring of only a few adults. If this is the case, the dispersal capabilities of nymphs by swimming, crawling or drift may be minimal even within a single stream.

Genetic differentiation and dispersal among populations of Paratya australiensis (Atyidae) in rainforest streams in southeast Queensland, Australia

We used measures of genetic differentiation at seven allozyme loci to estimate the degree of movement of a stream invertebrate within and between catchments. Populations of Paratya australiensis, a common atyid shrimp, were sampled from three rainforest streams from each of two subcatchments in two adjacent drainage systems in southeast Queensland. Marked genetic differentiation was observed at all loci, suggesting extremely limited movement on a small spatial scale. This result is surprising given the widespread geographic distribution of P. australiensis in Australia, its great abundance in headwater streams in southeast Queensland, and the presence of a planktonic larval stage. Large differences in genetic structure occurred between streams, in some instances between those in the same subcatchment. Even larger genetic differences were seen between samples from streams in different subcatchments, with alternative alleles being fixed at different sites. The greatest differences were not, however, between the two drainage systems as predicted by the stream hierarchy model. This extreme spatial structuring was remarkably stable over a two-year period.

Concordance between dispersal and mitochondrial gene flow: isolation by distance in a tropical teleost, Lates calcarifer (Australian barramundi)

Patterns of population subdivision and the relationship between gene flow and geographical distance in the tropical estuarine fish Lates calcarifer (Centropomidae) were investigated using mtDNA control region sequences. Sixty-three putative haplotypes were resolved from a total of 270 individuals from nine localities within three geographical regions spanning the north Australian coastline. Despite a continuous estuarine distribution throughout the sampled range, no haplotypes were shared among regions. However, within regions, common haplotypes were often shared among localities. Both sequence-based (average ΦST=0.328) and haplotype-based (average Φ ST=0.182) population subdivision analyses indicated strong geographical structuring. Depending on the method of calculation, geographical distance explained either 79 per cent (sequence-based) or 23 per cent (haplotype-based) of the variation in mitochondrial gene flow. Such relationships suggest that genetic differentiation of L. calcarifer has been generated via isolation-by-distance, possibly in a stepping-stone fashion. This pattern of genetic structure is concordant with expectations based on the life history of L. calcarifer and direct studies of its dispersal patterns. Mitochondrial DNA variation, although generally in agreement with patterns of allozyme variation, detected population subdivision at smaller spatial scales. Our analysis of mtDNA variation in L. calcarifer confirms that population genetic models can detect population structure of not only evolutionary significance but also of demographic significance. Further, it demonstrates the power of inferring such structure from hypervariable markers, which correspond to small effective population sizes.

Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life history transition in phylogeographic diversification

The widespread distribution of the freshwater shrimp Paratya australiensis in eastern Australia suggests that populations of this species have been connected in the past. Amphidromy is ancestral in these shrimps, although many extant populations are known to be restricted to freshwater habitats. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to examine diversity within P. australiensis and to assess the relative importance of amphidromy in its evolutionary history. We hypothesized that if transitions from an amphidromous to a freshwater life history were important, then we would find a number of divergent lineages restricted to single or groups of nearby drainages. Alternatively, if amphidromy was maintained within the species historically, we expected to find lineages distributed over many drainages. We assumed that the only way for divergence to occur within amphidromous lineages was if dispersal was limited to between nearby estuaries, which, during arid periods in the earths history, became isolated from one another. We found nine highly divergent mtDNA lineages, estimated to have diverged from one another in the late Miocene/early Pliocene, when the climate was more arid than at present. Despite this, the geographic distribution of lineages and haplotypes within lineages did not support the notion of a stepping‐stone model of dispersal between estuaries. We conclude that the extensive divergence has most likely arisen through a number of independent amphidromy–freshwater life history transitions, rather than via historical isolation of amphidromy populations. We also found evidence for extensive movement between coastal and inland drainages, supporting the notion that secondary contact between lineages may have occurred as a result of drainage rearrangements. Finally, our data indicate that P. australiensis is likely a complex of cryptic species, some of which are widely distributed, and others geographically restricted.

Regional patterns of genetic structure among Australian populations of the mud crab, Scylla serrata (Crustacea : Decapoda): evidence from mitochondrial DNA

The population genetic structure of the estuarine crab, Scylla serrata (Forskal, 1775), was examined among shelf-connected locations and across a historical bio-geographic barrier. Over 300 individuals were sampled from multiple locations within coastal regions (western, northern and eastern) of Australia and analysed for mutational differences at a mitochondrial coding gene (COI). Analysis of molecular variance indicated mitochondrial haplotypes to be structured regionally (P < 0.001), which contrasted with evidence of genetic panmixia within regions. Regional genetic structure broadly correlated with hydrological circulation, supporting the contention that release of propagules away from the estuary may allow genetic connectivity among widespread shelf-connected S. serrata populations. That similar patterns of maternal gene flow are absent among trans-oceanic populations may indicate that the spatial scale of effective dispersal for this species is generally limited to areas of coastal shelf. Two distinct clades of haplotypes were geographically separated either side of the Torres Strait, a narrow sea channel connecting the northern and eastern regions of coastal Australia. This pattern of historical genetic separation is concordant with a number of other marine species across northern Australia and may indicate a shared history of vicariance induced by eustasy. Alternatively, we suggest that sundering of S. serrata populations resulting in cladogenesis may have its origins outside of the northern Australian region.