John K. Jackson

Can DNA barcodes of stream macroinvertebrates improve descriptions of community structure and water quality

Abstract Four approaches to or levels of identifying macroinvertebrates (amateur/family, expert entomologist/genus, expert entomologist/genus–species, and DNA barcoding/species) were used to assess community structure and water quality in White Clay Creek, Pennsylvania, USA. Macroinvertebrates were collected in March 2008 from 2 riffle sites 3.9 km apart on the same stream. The downstream site was known to be degraded by land and water use. About 98% of the 1617 specimens used for analysis, including small, immature, and damaged specimens, were successfully barcoded (sequenced) for the mitochondrial cytochrome c oxidase subunit I gene. A criterion of 2 to 4% genetic divergence provided good separation of presumptive species. Barcodes increased the taxonomic inventory across the 2 sites by 475% (124 taxa) relative to the amateur level, and 125% (83 taxa) and 70% (62 taxa) relative to the expert genus and species levels, respectively. Barcoding revealed species not currently described in larval taxonomic keys, including multiple (2–11) coexisting congeneric species. That 150 species were revealed by barcoding samples collected on the same date and in the same habitat was unprecedented, as was the fact that 60 cm2 of stream bottom supported an average of 248 to 347 individuals representing 55 to 68 species. Most barcode species were rare, with 42% represented by ≤2 individuals. Across all species, 43 of 89 barcode species were unique to upstream site 11 and 60 of 107 were unique to downstream site 12. In terms of water-quality assessment, most of the 17 metrics studied changed significantly (α  =  0.05) when taxonomy changed from family to genus–species (79% and 93% for sites 11 and 12, respectively), and many also changed when taxonomy changed from genus to species (59 and 65% for sites 11 and 12, respectively). The proportion of metrics able to detect a difference (α  =  0.05) between sites 11 and 12 increased with improved taxonomic resolution (36, 47, 65, and 76% for family, genus, genus–species, and barcode, respectively). The results revealed a pollution-tolerance gap because barcoding pushed larval taxonomy beyond the available pollution-tolerance data. Regardless, the combined morphological and molecular approach provides a finer resolution for evaluating environmental change associated with both natural and anthropogenic processes. The ability to distinguish larvae at the species level through barcoding finally puts biodiversity assessments for aquatic communities in terms comparable to those used for terrestrial ecosystems where estimates of biodiversity for plants and animals are never quantified at the level of genus or family. We conclude that DNA barcodes of stream macroinvertebrates will improve descriptions of community structure and water quality for both ecological and bioassessment purposes.

Egg and Larval Development Times for 35 Species of Tropical Stream Insects from Costa Rica

We examined total development times for 5 mayfly species, 2 stoneflies, 10 caddisflies, and 18 chironomid midges collected from three streams that flow through tropical evergreen forest in northwestern Costa Rica. Most eggs, larvae, and pupae were reared in the laboratory in a photoperiod of 12:12 LD and at 20°C, which simulated field conditions. Algae, algal detritus, and leaves were provided as food for all species; predators were also given various animal prey. All study species had total development times that were rapid relative to the univoltine life histories observed or assumed for many temperate species. Egg development times ranged from a few days to approximately a week for chironomids and from 10 to 38 days for mayflies, stoneflies, and caddisflies. Most chironomids had short larval/pupal development times: development was completed in 19-29 d by seven species, in 30-40 d by nine species, and in >50 d by two species. Relatively short development times (including the pupal stage when present) were also observed for the mayfly Acerpenna sp. (28 d) and the caddisflies Wormaldia sp. (45 d) and Oecetis nr. prolongata (52 d). Larval/pupal development times were longer for the other four mayflies (76-159 d), two stoneflies (83-167 d), and eight caddisflies (72-209 d). No evidence of egg or larval diapause was observed. The combination of rapid development and absence of diapause suggests that all these species have multivoltine life histories. This finding has important implications for temporal changes in the structure and function of the aquatic insect assemblage in these streams.

Climate Change and the Life Histories and Biogeography of Aquatic Insects in Eastern North America

One of the most important factors affecting the life history characteristics and biogeography of aquatic insects is temperature (Sweeney, 1984). Insects are poikilothermic (cold-blooded) animals whose metabolism, rate and magnitude of growth, development, and overall behavioral activities respond significantly to thermal change on a diel, seasonal, and annual basis (Ward and Stanford, 1982). Despite this sensitivity to temperature, most aquatic insect species can be found in aquatic habitats over a broad geographic area that includes a wide range of thermal regimes. Obviously, these aquatic insect species possess bioenergetic, developmental, and/or behavioral mechanisms that enable conspecific populations to survive and reproduce in very different environmental conditions.

Concentrations and Export of Solutes from Six Mountain Streams in Northwestern Costa Rica

Streamwater chemistry in six streams draining adjacent, undisturbed catchments of volcanic origin in northwestern Costa Rica was monitored between 1990 and 1993. The catchments ranged from 0.36 to 3.2 km2 in area, and from 600 to 1300 m in elevation. Rainfall averaged 2.4 m/yr at 600 m but was unmeasured and probably much greater at higher elevations. Runoff among the catchments ranged from 1.4 to 4.3 m/yr, with approximately 84% occurring during the May-December rainy season. Within individual streams, concentrations of NO3-, total dissolved phosphorus (TDP), and dissolved organic carbon (DOC) increased with streamflow while Ca2+, Mg2+, and Na+ decreased with streamflow. K+ showed little response to streamflow. Among streams, flow-weighted mean concentrations of NO3- (0.12-0.30 mg/L), DOC (0.63-1.79 mg/L), and TDP (0.008-0.029 mg/L) were intercorrelated and varied inversely with annual runoff. DOC concentrations were low compared with data from other tropical streams. Annual exports (kg ha-1yr-1) for these solutes were relatively uniform among catchments, suggesting that differences in runoff explain much of the stream-to-stream differences in solute concentrations. Cation exports were also relatively uniform among five of the streams, but were distinctly higher in the remaining stream, which is also enriched in SO42- and Cl-, and may receive water from a geothermal source.

Present Status and Future Directions of Tropical Stream Research

This paper presents the results of a survey of our understanding of the structure and function of streams and rivers based on the opinions of colleagues working in the tropics. The questionnaire examined the status of eight general topics: taxonomy, life history traits, standing crop biomass, production, trophic structure, transport/drift of material or organisms, nutrient dynamics, and biotic interactions. Two conclusions were reached: (1) significant progress has been made in our understanding of tropical streams and rivers; very few subjects have not been examined at one or more tropical locations. (2) Although most subjects have received at least some attention, they remain relatively unknown at most sites. Recommendations for future directions in tropical stream research are given.

Organic matter transport in New York City drinking-water-supply watersheds

Abstract Organic matter (OM) in streams that provide drinking water is a potential energy source for bacterial regrowth in distribution systems and a precursor for disinfection byproducts. Baseflow concentrations of OM were measured over a 3-y period in 60 streams divided evenly between water-supply regions east and west of the Hudson River (EOH or WOH) in New York State. A baseline of OM concentrations in the 2 regions was generated, and land use/cover variables were related to those baseline concentrations. Dissolved organic C (DOC), biodegradable DOC (BDOC), and particulate OM (POM) reflected regional differences in land use and point-source discharges. Three-year mean concentrations for these variables and for total organic C (TOC) were significantly lower in the WOH than in the EOH by factors of 1.5 to 2.3. Size fractionation of POM showed similarities between regions with >70% of particles in the 0.5- to 10-μm size class. DOC made up most of the TOC in both regions, and DOC:POC ratios ranged from 1.7 to 54.4. Stepwise multiple linear regressions revealed that agriculture and forest land uses explained most of the variation in OM concentrations in the WOH, whereas wetlands and point-source discharges, primarily associated with wastewater treatment plants, explained most of the variation in OM concentrations in the EOH. Despite the potential problems from OM for drinking water quality, OM is a natural and important component of stream ecosystems, so its total elimination from watersheds is neither advisable nor possible. Our data from watersheds in the WOH region with high percentages (>97%) of forested land use and from small to mid-sized watersheds in the EOH with no point-source discharges provide lower limits for OM concentrations and targets for best management practices.

Semivoltinism, Seasonal Emergence, and Adult Size Variation in a Tropical Stream Mayfly (Euthyplocia hecuba)

Life history characteristics of the stream mayfly Euthyplocia hecuba (Hagen) (Polymitarcyidae:Euthyplociinae) were studied over a 4-yr period in two tropical streams (Río Tempisquito and Quebrada Marilin) draining primary evergreen forest in northern Costa Rica. Larvae burrow in the substratum of the stream, living under small to large cobbles that are firmly embedded in the stream bottom. Euthyplocia hecuba is sexually dimorphic and one of the largest mayflies of Central America, with maximum larval size of 149 mg (dry mass) for females and 35 mg for males. Mature female and male larvae are about 40% larger in Q. Marilin relative to R. Tempisquito. Subimagoes emerge about 1 h before dawn (∼0400 h); the molt to the imago (or true adult stage) occurs ∼20 min later. Adult emergence and reproduction occurs mainly between June and November. Females mate and then oviposit in riffle areas just before dawn, with the time period gradually changing from 0446 and 0507 h in June to 0508 and 0529 h in October. We found that size of adult males and females gradually declined during the emergence period. Fecundity averaged 984 in October (range 364-2851), with eggs being very large for a mayfly (0.46 × 0.4 mm; 0.017 mg dry mass). The proportion of adult biomass allocated to eggs (reproductive effort) averaged 0.51 but varied according to female size. Median egg development time was 113, 55, and 31 d at 15, 20, and 25°C. The hatch success of eggs was >90% at 15 and 20°C, only 68% at 25°C, and 0% at 10 and 30°C. First instar larvae are relatively large for a mayfly, having a head width of 0.11 mm and a body length of 1.30 mm. Seasonal changes in larval size distribution suggest that larval development takes ∼22 mo to complete and may involve a developmental quiescence or diapause during the first year. A 2-yr life history appears to be the most parsimonious hypothesis given a 2-mo egg development time, the occurrence of two size cohorts of larvae throughout most of the year, and the temporal pattern of maximum and average larval sizes over the course of the sampling period. Our data suggest that seasonality in the developmental dynamics of larvae underlies both the seasonal emergence and decline in dry mass of both adult males and females during the emergence period. The data provide the first evidence for semivoltinism in a tropical mayfly.

Cryptic Biodiversity in Streams: A Comparison of Macroinvertebrate Communities Based on Morphological and DNA Barcode Identifications

Abstract: Species-level identifications are difficult or impossible for many larval aquatic macroinvertebrates. We described the taxonomic composition of macroinvertebrate communities from 5 coastal streams in 3 neighboring catchments in southern California. We compared taxonomic identifications based on deoxyribonucleic acid (DNA) barcoding (cytochrome c oxidase subunit I [COI]) with morphological identifications of the same specimens. We examined 5870 individuals, and barcodes with sequence lengths >350 base pairs (bp) for 91% of those specimens. We used the naturally occurring gaps in divergence frequencies for each order (usually 2% level of genetic divergence) to delimit putative species for all taxonomic groups except Simulium (3%) and Baetis (1%). We identified 200 species across these 5 streams. We identified 104 more species via barcodes than via morphology (200 vs 96, a 108% increase). Richness increases were greatest for Chironomidae (60 more species), Ephemeroptera (10 species), Acari (10 species), and Trichoptera (6 species). Forty-five percent of the genera/species identified morphologically represented >2 species. Many (86) species identified with barcodes were represented by only 1 or 2 specimens and were found at only 1 stream. Thus, species rarity (either spatially or numerically) appears to be a common characteristic of these streams. Barcoding increased total richness at each site by 12 to 40 taxa over morphology alone, and increased the difference between reference and impact sites in terms of lost taxa. These results suggest that macroinvertebrate biodiversity in streams has been underestimated substantially in the past, as has the biodiversity lost in response to environmental stress. The potential of DNA barcoding will not be fully realized until we can assign traits, such as habitat preference, ecological function, and pollution tolerance, at the species level.

Taxonomy and genetics of the parthenogenetic mayfly Centroptilum triangulifer and its sexual sister Centroptilum alamance (Ephemeroptera:Baetidae)

Abstract Allozymes were used to examine population genetic structure and species boundaries in the clonal, obligately parthenogenetic Centroptilum triangulifer and its sexual sister species Centroptilum alamance from 3 sites in Pennsylvania and 1 site in North Carolina, USA. Genotype frequencies in field populations of C. triangulifer showed numerous departures from Hardy–Weinberg expectations (mostly heterozygote excesses) and significant linkage disequilibrium at most testable locus combinations, as expected for a clonal parthenogen. A total of 51 distinct clones of C. triangulifer was identified, some of which were found at multiple sites (separated by >700 km in one case). Each stream contained from 7 to 25 clones and clonal frequencies at a given site varied greatly over time. Allelic patterns in laboratory hybrids suggest that parthenogenesis in C. triangulifer is diploid and automictic, and that crossing over is suppressed. In contrast, C. alamance populations had only a few Hardy–Weinberg departures (all heterzygote deficiences) and little or no linkage disequilibrium. No published work provides characters to distinguish the 2 species, but our data support retention of specific status for C. triangulifer and C. alamance because: 1) consistent, fixed allelic differences were found over a broad geographic area (>700 km) with no evidence of introgression despite co-occurrence (sympatry) in the same stream, 2) laboratory hybridization experiments demonstrated the existence of postzygotic barriers to gene flow between the species, and 3) measures of both interspecific and intraspecific genetic similarity were comparable to those found between other mayfly species. Phylogenetic analysis of the genetic data suggests speciation preceded the transition to obligate parthenogenetic reproduction in C. triangulifer. Morphological examination of genetically identified specimens enabled us to describe subtle but consistent differences that can be used to distinguish the species. Thus, what initially appeared to be single populations with skewed sex ratios (7, 11, and 24% male) at 3 of our study sites was, in fact, 2 populations at each site—1 exclusively female (C. triangulifer) and the other a normal, sexual (1:1 sex ratio) population (C. alamance). A similar approach, combining detailed genetic and breeding experiments with close morphological study, could help resolve taxonomic problems in some of the numerous other bisexual/parthenogenetic mayfly taxa.

Does DNA barcoding improve performance of traditional stream bioassessment metrics

Abstract: Benthic macroinvertebrate community composition is used to assess wetland and stream condition and to help differentiate the effects of stressors among sites. Deoxyribonucleic acid (DNA) barcoding has been promoted as a way to increase taxonomic resolution and, thereby, to increase the sensitivity of bioassessment metrics. We compared the ability of several commonly used bioassessment metrics calculated with data derived from morphology and from DNA barcoding to detect differences in stream condition of 6 paired sites in southern California with relatively subtle impacts to habitat. At each site, we sampled an upstream (reference) reach and a downstream (impact) reach with armored stream banks. We counted and identified ∼600 organisms/ sample based on morphology (generally to species, but to genus for midges). We then extracted mitochondrial (mt)DNA from each individual and sequenced the ∼658-base pair (bp) barcoding region of the cytochrome c oxidase subunit I (COI) gene. Most (91%) organisms yielded sequences >350 bp in length, but high failure rates for all taxa collected from 1 stream required that we exclude it from analysis. Sixteen metrics calculated with morphological data showed subtle but not significant differences in community composition between armored and unarmored reaches. The statistical power of 10 of the 16 metrics was substantially higher when calculated with DNA than with morphological data, and we were able to discern differences between armored and unarmored reaches with the DNA data. These differences were associated with increased taxonomic richness detected for midges, mayflies, noninsects, caddisflies, and black flies when DNA data were used. Our results suggest that identifications based on DNA barcoding have the potential to improve power to detect small changes in stream condition.