Winsor H. Lowe

What can genetics tell us about population connectivity

Genetic data are often used to assess ‘population connectivity’ because it is difficult to measure dispersal directly at large spatial scales. Genetic connectivity, however, depends primarily on the absolute number of dispersers among populations, whereas demographic connectivity depends on the relative contributions to population growth rates of dispersal vs. local recruitment (i.e. survival and reproduction of residents). Although many questions are best answered with data on genetic connectivity, genetic data alone provide little information on demographic connectivity. The importance of demographic connectivity is clear when the elimination of immigration results in a shift from stable or positive population growth to negative population growth. Otherwise, the amount of dispersal required for demographic connectivity depends on the context (e.g. conservation or harvest management), and even high dispersal rates may not indicate demographic interdependence. Therefore, it is risky to infer the importance of demographic connectivity without information on local demographic rates and how those rates vary over time. Genetic methods can provide insight on demographic connectivity when combined with these local demographic rates, data on movement behaviour, or estimates of reproductive success of immigrants and residents. We also consider the strengths and limitations of genetic measures of connectivity and discuss three concepts of genetic connectivity that depend upon the evolutionary criteria of interest: inbreeding connectivity, drift connectivity, and adaptive connectivity. To conclude, we describe alternative approaches for assessing population connectivity, highlighting the value of combining genetic data with capture‐mark‐recapture methods or other direct measures of movement to elucidate the complex role of dispersal in natural populations.

Moving Headwater Streams to the Head of the Class

the establishment of the chemical signature for water quality in the landscape. High levels of habitat diversity among and within these small streams create niches for diverse organisms, including headwater-specialist species of aquatic invertebrates, amphibians, and fish. Headwaters also act as refugia for riverine species during specific life-history stages and critical periods of the year, such as warm summer months. Like the alveoli (the final branches of the respiratory tree that serve as the primary gas exchange units of the lungs), headwater streams are characterized by strong and vital interactions with the systems that surround them. Terrestrial inputs—dissolved nutrients, toxins, and particulate matter, for example—play a central role in determining the physical and chemical conditions of headwater streams (Likens and Bormann 1974) and in regulating the composition and productivity of biotic communities in these streams (Wallace et al. 1997). Because of this close terrestrial‐aquatic linkage, the ecosystem services provided by headwaters and the species they support tend to be very sensitive to natural and anthropogenic disturbance of surrounding lands. Along with other distinctive qualities, this close connection creates a unique set of challenges and opportunities related to the protection of headwaters, and to research in these systems. Conservation challenges and opportunities

Robust detection of rare species using environmental DNA: the importance of primer specificity.

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method’s sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. In this study we test factors that influence the specificity and sensitivity of TaqMan MGB assays using co-occurring, closely related brook trout (Salvelinus fontinalis) and bull trout (S. confluentus) as a case study. We found qPCR to be substantially more sensitive than traditional PCR, with a high probability of detection at concentrations as low as 0.5 target copies/µl. We also found that number and placement of base pair mismatches between the Taqman MGB assay and non-target templates was important to target specificity, and that specificity was most influenced by base pair mismatches in the primers, rather than in the probe. We found that insufficient specificity can result in both false positive and false negative results, particularly in the presence of abundant related species. Our results highlight the utility of qPCR as a highly sensitive eDNA tool, and underscore the importance of careful assay design.

Can't See the Forest for the Stream? In-stream Processing and Terrestrial Nitrogen Exports

Abstract There has been a long-term decline in nitrate (NO3−) concentration and export from several long-term monitoring watersheds in New England that cannot be explained by current terrestrial ecosystem models. A number of potential causes for this nitrogen (N) decline have been suggested, including changes in atmospheric chemistry, insect outbreaks, soil frost, and interannual climate fluctuations. In-stream removal of NO3− has not been included in current attempts to explain this regional decline in watershed NO3− export, yet streams may have high removal rates of NO3−. We make use of 40 years of data on watershed N export and stream N biogeochemistry from the Hubbard Brook Experimental Forest (HBEF) to determine (a) whether there have been changes in HBEF stream N cycling over the last four decades and (b) whether these changes are of sufficient magnitude to help explain a substantial proportion of the unexplained regional decline in NO3− export. Examining how the tempos and modes of change are distinct for upland forest and stream ecosystems is a necessary step for improving predictions of watershed exports.

Linking Scales in Stream Ecology

Abstract The hierarchical structure of natural systems can be useful in designing ecological studies that are informative at multiple spatial scales. Although stream systems have long been recognized as having a hierarchical spatial structure, there is a need for more empirical research that exploits this structure to generate an understanding of population biology, community ecology, and species–ecosystem linkages across spatial scales. We review studies that link pattern and process across multiple scales of stream-habitat organization, highlighting the insight derived from this multiscale approach and the role that mechanistic hypotheses play in its successful application. We also describe a frontier in stream research that relies on this multiscale approach: assessing the consequences and mechanisms of ecological processes occurring at the network scale. Broader use of this approach will advance many goals in applied stream ecology, including the design of reserves to protect stream biodiversity and the conservation of freshwater resources and services.

Use of multiple dispersal pathways facilitates amphibian persistence in stream networks

Although populations of amphibians are declining worldwide, there is no evidence that salamanders occupying small streams are experiencing enigmatic declines, and populations of these species seem stable. Theory predicts that dispersal through multiple pathways can stabilize populations, preventing extinction in habitat networks. However, empirical data to support this prediction are absent for most species, especially those at risk of decline. Our mark-recapture study of stream salamanders reveals both a strong upstream bias in dispersal and a surprisingly high rate of overland dispersal to adjacent headwater streams. This evidence of route-dependent variation in dispersal rates suggests a spatial mechanism for population stability in headwater-stream salamanders. Our results link the movement behavior of stream salamanders to network topology, and they underscore the importance of identifying and protecting critical dispersal pathways when addressing region-wide population declines.

Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams.

Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid‐summer through autumn, over flows ranging from approximately 1–96 L/s. We used quantitative PCR to relate DNA copy number to distance from source. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were highest close to the source and quickly trailed off over distance. At the highest flows, DNA counts were relatively low both near and far from the source. Biomass was positively related to eDNA copy number in both streams. A combination of cell settling, turbulence and dilution effects is probably responsible for our observations. Additionally, during high leaf deposition periods, the presence of inhibitors resulted in no amplification for high copy number samples in the absence of an inhibition‐releasing strategy, demonstrating the necessity to carefully consider inhibition in eDNA analysis.

LINKING DISPERSAL TO LOCAL POPULATION DYNAMICS: A CASE STUDY USING A HEADWATER SALAMANDER SYSTEM

Dispersal can strongly influence local population dynamics and may be critical to species persistence in fragmented landscapes. Theory predicts that dispersal by resident stream organisms is necessary to offset the loss of individuals to downstream drift. However, there is a lack of empirical data linking dispersal and drift to local population dynamics in streams, leading to uncertainty regarding the general demographic significance of these processes and the power of drift to explain observed dispersal patterns. I assessed the contribution of dispersal along a first-order stream to population dynamics of the headwater salamander Gyrinophilus porphyriticus (Plethodontidae). I conducted mark–recapture surveys of two contiguous 500 m long sections of a study stream in June, July, and August of 1999, 2000, and 2001. Movement by G. porphyriticus larvae and adults showed a strong upstream bias in the study stream, as well as in 11 other streams that I surveyed. Using mark–recapture models and Akaikes informa...

Linking direct and indirect data on dispersal: isolation by slope in a headwater stream salamander.

There is growing recognition of the need to incorporate information on movement behavior in landscape-scale studies of dispersal. One way to do this is by using indirect indices of dispersal (e.g., genetic differentiation) to test predictions derived from direct data on movement behavior. Mark-recapture studies documented upstream-biased movement in the salamander Gyrinophilus porphyriticus (Plethodontidae). Based on this information, we hypothesized that gene flow in G. porphyriticus is affected by the slope of the stream. Specifically, because the energy required for upstream dispersal is positively related to slope, we predicted gene flow to be negatively related to change in elevation between sampling sites. Using amplified DNA fragment length polymorphisms among tissue samples from paired sites in nine streams in the Hubbard Brook Watershed, New Hampshire, USA, we found that genetic distances between downstream and upstream sites were positively related to change in elevation over standardized 1-km distances. This pattern of isolation by slope elucidates controls on population connectivity in stream networks and underscores the potential for specific behaviors to affect the genetic structure of species at the landscape scale. More broadly, our results show the value of combining direct data on movement behavior and indirect indices to assess patterns and consequences of dispersal in spatially complex ecosystems.

Network analysis reveals multiscale controls on streamwater chemistry

Significance Headwater streams are important sources of water for downstream ecosystems and human communities. These streams comprise the vast majority of stream and river kilometers in watersheds and affect regional water quality. However, the actual spatial variation of water quality in headwater streams is often unknown. Our study uses an unusually high-resolution spatial dataset from a headwater stream network and employs a statistical tool to objectively describe spatial patterns of streamwater chemistry within a stream network. This approach provides insights on how flowing water interacts with vegetation, soil, and geologic materials in the surrounding landscape. Application of this method may help to identify factors impairing water quality and to inform strategies for protecting aquatic ecosystems. By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.