TL;DR: This study is the first to the authors' knowledge to successfully employ an eDNA approach to detect rare or threatened invertebrates from subterranean ecosystems, including accounting for PCR inhibition and the potential for cryptic genetic diversity.
Abstract: Effective conservation and management of biodiversity is limited by a lack of critical knowledge on species’ distributions and abundances. This problem is particularly exacerbated for species living in habitats that are exceptionally difficult to access or survey, such as groundwater habitats. Environmental DNA (eDNA) represents a rapid, noninvasive, and potentially cost-effective new tool for detection and monitoring of biodiversity that occur in such habitats. In this study, we investigated the utility of eDNA in detecting the federally endangered Hay’s Spring Amphipod Stygobromus hayi and a co-occurring common congener S. tenuis potomacus from unique groundwater-associated habitats—hypotelminorheic seepage springs—in the Washington, DC metro area. We developed taxon-specific primers and probes for each species to amplify Stygobromus DNA using qPCR. In silico and in vitro validation demonstrated specificity of each designed assay. Assays were then used to screen water samples collected from ten seepage springs. Stygobromus hayi was detected at four seepage springs, including one potential new locality, while S. t. potomacus was detected at four springs, two of which were new localities. This study is the first to our knowledge to successfully employ an eDNA approach to detect rare or threatened invertebrates from subterranean ecosystems. Our study highlights challenges of employing an eDNA approach for the detection and monitoring of invertebrates in groundwater habitats that are difficult to study, including accounting for PCR inhibition and the potential for cryptic genetic diversity.
TL;DR: The underground amphipod fauna of North America is highly diverse and presently includes 169 species representing 28 genera in 10 families or family groups as discussed by the authors, and three major zoogeographic patterns are recognized among subterranean amphipods in North America: (1) ancient freshwater distribution; (2) marine relict distribution; and (3) marine brackish water distribution.
Abstract: The subterranean amphipod fauna of North America is highly diverse and presently includes 169 species representing 28 genera in 10 families or family groups. The vast majority of these species are stygobionts (i.e. obligate dwellers in aquatic subterranean habitats). Three major zoogeographic patterns are recognized among subterranean amphipods in North America: (1) ancient freshwater distribution; (2) marine relict distribution; and (3) marine-brackish water distribution. Taxa with pattern 1 distribution are exclusively freshwater forms restricted to the Holarctic region and have no known marine relatives. The large, exclusively subterranean genus Stygobromus (Crangonyctidae) is a principal example. Taxa with pattern 2 distribution are exclusively freshwater forms but have close relatives in marine/brackish water and are believed to have been derived from marine ancestors by stranding during marine transgressions in Late Cretaceous and Tertiary times. The weckeliid group of Hadziidae is a principal example. Taxa with pattern 3 distribution live at present in habitats ranging from fully marine to marginally fresh waters on and around islands in the West Indies, where they are believed to have become isolated during emergence of island groups in middle to late Cenozoic times. The genus Metaniphargus (Hadziidae) is a principal example.
TL;DR: A revised diagnosis of the genus Stygobromus is given, accompanied by a redescription of S. hubbsi Shoemaker from Oregon and the descriptions of 17 new species from the western United States.
Abstract: Holsinger, John R. Systematics of the Subterranean Amphipod Genus Stygobromus (Gammaridae), Part I: Species of the Western United States. Smithsonian Contributions to Zoology, number 160, 63 pages, 37 figures, 1974.—The subterranean amphipod genus Stygobromus is restricted to North America with the exception of one poorly known species from Siberia. Stygobromus is a member of the Crangonyx group of the family Gammaridae and is closely related to two other North American subterranean genera—Apocrangonyx and Stygonectes. It also has a close affinity with the Holarctic genus Synurella. Species of Stygobromus are widely distributed in cave waters and related ground water habitats throughout the greater part of the cavernous regions of the eastern, middle western, and far western United States. A revised diagnosis of the genus is given, accompanied by a redescription of S. hubbsi Shoemaker from Oregon and the descriptions of 17 new species from the western United States. Of the 18 species recorded from the West, 15 belong to the newly erected hubbsi group. Stygobromus putealis (Holmes) from wells in Wisconsin is also assigned to this evolutionary group. Members of the hubbsi group are closely allied morphologically and are assumed to have been derived from a common ancestor. The western species inhabit a variety of subterranean biotopes, including limestone and lava caves, wells, springs, and one deep lake. OFFICIAL PUBLICATION DATE is handstamped in a limited number of initial copies and is recorded in the Institution's annual report, Smithsonian Year. SI PRESS NUMBER 4926. SERIES COVER DESIGN: The coral Montastrea cavernosa (Linnaeus). Library of Congress Cataloging in Publication Data Holsinger, John R. Systematics of the subterranean amphipod genus Stygobromus (Gammaridae) (Smithsonian contributions to zoology, no. 160) Bibliography: p.
TL;DR: In this paper, a grid of shallow sampling wells penetrating the alluvial floodplain aquifer (ca. 10 m × 5 km × 10 km) of the Flathead River, Montana, USA was used to identify the most common crustaceans.
Abstract: Interstitial crustaceans were collected from a grid of shallow sampling wells penetrating the alluvial floodplain aquifer (ca. 10 m × 5 km × 10 km) of the Flathead River, Montana, USA. Eighteen taxa were identified, which collectively encompassed a range of hypogean-epigean affinities. The subterranean amphipod Stygobromus spp., the most common crustacean, occurred in all wells but was rare in the channel well. When well data were pooled into ‘habitat types’ (channel, bank, near-, central-, and far-floodplain), distinct faunal patterns were apparent. Crustaceans constituted an increasing percentage of the total interstitial fauna from the channel to the near-floodplain, then maintained similar relative abundance levels with increasing distance from the river. Stygobionts attained maximum values at near- and central-floodplain habitats where copepods and ostracods dropped to the lowest levels. Distribution and abundance patterns of Crustacea at the floodplain scale are structured by hydrogeologic and geomorphic processes reflected only in part by distance from the river channel. The flood plain appears to contain a latticework of alluvial-filled paleochannels of high hydraulic conductivity that induce spatial discontinuities within the aquifer and that may play an important role in determining crustacean distribution patterns.