DOI: 10.6078/d15d9c
title: Ecological consequences of shifting habitat mosaics within and across years in an intermittent stream

description: Intermittent streams that cease to flow during dry periods represent more
 than half of the global river network and are particularly common in arid
 and semi-arid regions. They are characterized by high spatial and temporal
 variability in aquatic habitat, forming a shifting habitat mosaic that
 supports diverse assemblages of native and endemic species. Climate
 projections for much of the world predict greater variation in
 precipitation and increasing drought severity, suggesting a need to better
 understand species’ responses to habitat variability within intermittent
 stream ecosystems. Here we explored changes in the distribution and
 abundance of aquatic vertebrates in response to a wide range of annual
 hydrologic conditions within a Mediterranean-climate intermittent stream
 in California. We conducted wetted habitat and vertebrate abundance
 surveys during the dry season for seven years, spanning both extreme wet
 and extreme dry annual precipitation conditions, and characterized the
 variation in the size, persistence, and spatial configuration of wetted
 habitats in relation to the observed abundance and composition of fishes,
 amphibians, and aquatic reptiles. We characterized the habitat mosaic
 using a k-means clustering approach and identified three habitat types
 with distinct size, persistence, and connectivity distributions. We found
 that some wetted habitat units persisted across all years, regardless of
 antecedent precipitation, whereas others dried in all but the wettest
 years. We determined that persistent pools, a subset of wetted habitats
 present in the stream, support diverse assemblages of native species even
 during extreme dry conditions, while transient pools act as important
 habitat for particular species and life stages, including a young-of-year
 minnow species. Linear mixed models indicated that species’ abundances
 were influenced by habitat quantity, quality, and connectivity. Our
 results suggest that intermittent streams can be characterized as shifting
 habitat mosaics that support unique species and life stages across space
 and time and play an important role in maintaining regional aquatic
 biodiversity.
description: <strong>Dataset Collection</strong>
 <strong>Wetted Channel Surveys</strong>
 We conducted surveys of wetted habitat conditions from 2014 to
 2021 (except 2020, due to Covid-19 restrictions) along the 5-kilometer
 study reach in Coyote Creek (Figure 1b). In 2014, we surveyed at the end
 of the dry season (i.e., September; Bogan et al. 2019). Beginning in 2015,
 we expanded the study to include monthly surveys from the onset of
 disconnection (typically July or August) through the end of the dry season
 (i.e., until the first autumn rainfall, typically October or November).
 The timespan within which surveys were conducted encompassed extreme low
 (2021: 263 mm) and high (2017: 1011 mm) precipitation years, including the
 final years of a statewide multi-year drought between 2012-2016, capturing
 the wide range of interannual hydrologic variability observed in the
 system. Between 2014-2016, monthly wet-dry mapping
 surveys were conducted by field crews walking the channel with a handheld
 Garmin eTrex GPS unit (+/- 15 m accuracy) and recording the coordinates at
 every point of surface water disconnection and reconnection along the
 channel. Disconnected reaches were defined as portions of the stream
 channel where there was a break in continuous surface water connectivity,
 with surface water patches being at least 1 m in length and &gt; 0.10
 meters deep. These coordinates were then used to digitize a streamline in
 ArcGIS 10.7.1 representing wet and dry reaches at each survey. Between
 2017-2021, surveys were conducted by field crews using a Bad Elf GPS (+/-
 1 m accuracy) connected to ArcCollector 21.0.4 on a tablet, using the same
 methods to map the presence of surface water. This latter method
 automatically digitizes and georeferences the wet and dry reaches along
 the stream. We used these data to create monthly maps of wetted habitat
 conditions across all years of the study.
 <strong>Habitat and Biological
 Surveys</strong> Along our 5-kilometer study
 stretch where we conducted wet-dry mapping, we identified five
 representative 250-meter reaches for more intensive habitat and biological
 sampling (Figure 1b). We conducted habitat and biological surveys for each
 wetted habitat unit within each 250-meter reach. A wetted habitat unit was
 defined as any disconnected surface water patch, which included both
 flowing reaches and isolated pools, with an area greater than 30 cm2. This
 size threshold was chosen as habitat patches smaller than 30 cm2 were
 unlikely to support aquatic vertebrate species. For each wetted habitat
 unit, presence and abundances of vertebrates were estimated using a rapid
 assessment approach, in which species abundance was estimated by visually
 scanning the wetted habitat unit for amphibians, reptiles, and fishes in
 the water column (see the complete taxa list on Table 1). Water clarity in
 Coyote Creek is generally high during the dry season, and species can be
 identified at depths of 2 m (Bogan et al., 2019). We also documented
 abundances of California floater mussels (Anodonta californiensis) because
 they are large (up to 12cm), have a life stage dependent upon freshwater
 fishes, and are of conservation concern. In addition to the visual
 assessment, we conducted spot sampling in undercut areas and along the
 benthos using a dip-net to identify benthic-oriented vertebrates. Each
 species observed was grouped into one of five abundance classes for
 analyses based on visual estimation: 1-10; 11-100; 101-500; 501-1000;
 &gt;1000 individuals. Visual estimation of abundance was completed by
 two observers (typically RAL and SMC). We distinguished between juvenile
 and adult life stages for some amphibians (Rana draytonii, red-legged
 frog; Rana boylii, yellow-legged frog) and fish (Hesperoleucus venustus,
 coastal roach; Catostomus occidentalis, Sacramento sucker; Ptychocheilus
 grandis, Sacramento pikeminnow). To standardize sampling effort among the
 units, the time spent sampling was proportional to the surface area of the
 habitat unit. For each wetted habitat unit, we
 collected and compiled a suite of metrics that relate to habitat
 suitability, including measures of quantity, quality, and connectivity. We
 measured the maximum length, maximum width, and maximum depth of each
 wetted habitat unit as habitat quantity metrics. We also calculated a
 series of connectivity measures for each habitat unit. These include
 distance to nearest patch, which is the Euclidean distance from the focal
 habitat unit to the nearest habitat unit, and distance to permanent pool,
 which is the Euclidean distance from the focal unit to the nearest
 permanent pool, which are a subset of pools that persisted during the
 driest conditions surveyed. Distance-weighted area was calculated as the
 distance to the nearest wetted habitat unit, divided by the area of the
 focal habitat unit. To characterize the long-term wetted persistence of
 the focal unit, we calculated the proportion of years in which the focal
 habitat unit had surface water in the month of September. Beginning in
 2017, we additionally measured several physicochemical parameters,
 including water temperature, dissolved oxygen, pH, and conductivity at
 each wetted habitat unit.