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Interagency Ecological Program San Francisco Estuary Larval Entrainment Study (LES)
Fish entrainment into California's State Water Project (SWP) and Central Valley Project (CVP) has been a source of mortality for native osmerid species, including Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys). While entrained adult and juvenile fishes are collected, identified and enumerated, the facilities design does not allow for a quantifiable estimate of larval fishes being entrained. This knowledge gap makes it difficult for managers to make scientifically informed decisions regarding the endangered Longfin & Delta Smelt. The Larval Entrainment Study (LES) aims to address this gap by providing a high-resolution dataset and insights into the variable abundances of Smelt at risk of entrainment, the community composition surrounding them, and associated water quality data. Our study design utilizes a variety of gear types and maximizes replicates to improve the understanding of larval Smelt abundances within the southern reach of the Sacramento and San Joaquin River Delta, the zone of entrainment for the SWP and CVP. Sampling began in 2022 using 10-minute stepped oblique tows of a Smelt Larval Survey (SLS) sled mounted with a 500 μm net. Tows were conducted in West Canal, outside Clifton Court Forebay (CCF), where the risk of entrainment is highest. Sampling was conducted five days a week in 2022 and three days a week in the following years. . Beginning in mid-January 2023, a 940 μm mesh net with the same dimensions as the SLS net was added, with sampling alternating between the two. This provided an intermediate gear between SLS (500 μm) and 20mm (1600 μm) nets. In 2024 we expanded to sample a transect of sites within the Old and Middle River (OMR) corridor. This provides broader spatial resolution and improves our ability to detect Osmerids within the South Delta. Sampling alternated between a high priority day (with intensive sampling in the lower San Joaquin River, SLS stations 809 & 812) and a longer transect day that ran
Interagency Ecological Program and US Fish and Wildlife Service: Enhanced Delta Smelt Monitoring Program Experimental Larval Survey Data 2018-2019
The United States Fish and Wildlife Service’s (USFWS) Experimental Larval Survey was designed and implemented by the Enhanced Delta Smelt Monitoring Program to assess alternative sampling methods for monitoring the larval life stages of the federally endangered Delta Smelt (Hypomesus transpacificus) within the San Francisco Estuary, California, USA. From 2018 to 2019, four different sampling methods (Beach Seine, Manta Trawl Net, 20-mm Surface Trawl Net, 20-mm Midwater Trawl Net) nested in time and space were used to estimate the occupancy rate, relative density, and size distribution of larval Delta Smelt across sampling methods and water depth strata within the San Francisco Estuary. For more information on the Lodi USFWS Office and the Enhanced Delta Smelt Monitoring Program: https://www.fws.gov/lodi/.
Relyea, R. A. 2001. Morphological and behavioral plasticity of larval anurans in response to different predators. Ecology 82:523-540.
Many organisms can adjust to a changing environment by developing alternative phenotypes that improve their fitness. Our understanding of phenotypic plasticity is largely based upon observations from single species responding to two different environments and measuring a single plastic trait. In this study, I examine predator-induced phenotypic plasticity in tadpoles by observing how six species of larval anurans respond to five different predator environments in 11 different traits (seven morphological traits, two behavioral traits, growth, and development). The results demonstrate that behavioral and morphological plasticity may be ubiquitous in larval anurans. The six prey species exhibited different responses to the same predator species, and each prey exhibited different responses to different predator species. This suggests that responses to a particular predator may not serve as general defense against all predators; rather, prey express predator-specific suites of responses. I also compared relative differences in plasticity among species and among traits. In contrast to earlier findings using only two predator environments, I found that different anurans possess similar degrees of plasticity for most of their traits when reared in a large number of environments. In addition, behavioral traits were always more plastic than morphological traits. Finally, I examined trait integration to address whether there were apparent trade-offs among traits and limits imposed by the abiotic environment. Trait integration, or the degree of correlated responses among traits across predator environments within a prey species, was very low. This further suggests that the suites of responses are predator specific and may be under independent directions of selection in different predator environments. Trait correlations across prey species indicated that there is an apparent trade-off between tail fin depth and body size. This relationship is supported by selection studies with
Relyea, R. A. 2001. The relationship between predation risk and anti-predator responses in larval anurans. Ecology 82:541-554.
Organisms that produce alternative, nondiscrete phenotypes in response to environmental conditions are expected to alter their phenotypes in relation to the degree of environmental change. This idea has been applied to the evolution of antipredator responses by prey, in which it has been hypothesized that prey should respond more strongly to predators that pose greater mortality risk. In a companion paper, I quantified predatorinduced behavioral and morphological responses in six species of larval anurans across five different predator environments and found that these responses were prey- and predatorspecific. In the present study, I addressed whether the responses were related to the level of predation risk posed by each of the predators. Within each prey species, I found that different predators posed different levels of predation risk; within each predator species, different prey species experienced different levels of risk. The differences in predation risk could be understood mechanistically after I quantified differences among predators in their ability to capture, handle, and consume prey and differences among prey in behavior and morphology. Using multivariate analyses, I found that predation risk had no significant effect on how a given prey responds to predators, although there were significant univariate behavioral effects; higher predation risk was related to greater decreases in activity and greater spatial avoidance. I also examined the relationship between risk and response across the six prey species within a predator treatment and found that higher predation risk across species leads to greater decreases in activity in the presence of Umbra and greater increases in tail depth in the presence of Anax. Thus, while previous studies have found relationships between predation risk and prey response when focusing on relatively few species, few predators, and a single trait, this more powerful test using 30 predator–prey combinations and nine traits sugge
Relyea, R. A. 2000. Trait-mediated indirect effects in larval anurans: Reversing competition with the threat of predation. Ecology 81:2278-2289.
Ecologists recently have been focusing on the role that trait-mediated indirect effects can have on community structure and composition. To date, this work has primarily focused on the effects of predator-induced behavioral plasticity on communities. However, predator-induced morphological plasticity, which has been documented in many taxa, might also lead to trait-mediated indirect effects. Here, I examined how predators altered the behavior and morphology of larval wood frogs (Rana sylvatica) and leopard frogs (R. pipiens) and how these phenotypic changes altered the outcome of competition between the two species. Competition in the absence of caged predators was asymmetric; when reared separately, leopard frogs grew more than wood frogs, but when competing (without predators), wood frogs grew faster than leopard frogs. The presence of caged predators reversed the outcome of competition between the two anuran prey. In the presence of larval dragonflies (Anax spp.) or caged mudminnows (Umbra limi), leopard frogs grew faster than wood frogs while total tadpole biomass production remained unchanged. Thus, there was a predator-mediated indirect effect. Because predators alter both the behavior and morphology of larval anurans and both of these traits are known to affect resource consumption and growth, both are potential mechanisms to explain the change in competitive outcome. Changes in behavior were not related to changes in growth, but changes in morphology (specifically mouth width and tail length) were related to changes in growth. When competitors were added (without predators), wood frogs increased their mouth width by 10% and their tail length by 3%, while leopard frogs increased their mouth width by 5% and did not change their tail length. The greater increase in mouth width for wood frogs should increase their forage intake, since tadpoles feed by scraping periphyton; the importance of a 3% longer tail in competitive ability is unknown. The presence of the p
Figure 13 - C. zonarius 1 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part II: Natural history: morphology, ecology, and behaviour, with accounts of larval ecology and insights into the aphytophagous C. dicksoni (Gabriel)
Figure 13 - C. zonarius 1st instar, in captivity, feeding on Osteospermum moniliferum (Silwerstroomstrand, Cape Town) in a manner described for C. zeuxo by Clark & Dickson (1971:168). The usual host plant for C. zonarius in nature is O. incanum.
Figure 1 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part II: Natural history: morphology, ecology, and behaviour, with accounts of larval ecology and insights into the aphytophagous C. dicksoni (Gabriel)
Figure 1 – Flattened components of male genitalia of eight Chrysoritis species. From top to bottom: juxta (furca), valve, and saccus. (a) C. thysbe, (b) C. p. pyroeis, (c) C. oreas, (d) C. zonarius, (e) C. f. felthami, (f) C. l. lycegenes, (g) C. dicksoni, and (h) C. phosphor. Reproduced from Heath (1997: 60). See also Fig. 2 in Heath et al., 2023.
Figure 3 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part II: Natural history: morphology, ecology, and behaviour, with accounts of larval ecology and insights into the aphytophagous C. dicksoni (Gabriel)
Figure 3 – Micrographs of basal hind wing scales at three magnifications, under dorso-lateral lighting intending to invoke iridescence if any. Images show the base of the wing. A–C: C. violescens (Komsberg Pass, sample SAM-LEP-A041390). D– F: C. aridus (Studer's Pass, SAM-LEP-A041391). G–I: C. amatola stat. nov. (Groot Winterberg, SAM-LEP-A041392). Images by S. van Noort.
Figure 7 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part II: Natural history: morphology, ecology, and behaviour, with accounts of larval ecology and insights into the aphytophagous C. dicksoni (Gabriel)
Figure 7 - Eggs of four Chrysoritis species (not to scale). A. C. z. zonarius (Churchhaven). B. C. rileyi (Brand Vlei). C. C. blencathrae (Waaihoek Mt.). D. C. dicksoni (Witsand; photo: S.E. Woodhall).
Figure 9 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part II: Natural history: morphology, ecology, and behaviour, with accounts of larval ecology and insights into the aphytophagous C. dicksoni (Gabriel)
Figure 9 – Four tubercles (excluding tentacular organ) re-drawn from Clark & Dickson (1971). (a) C. nigricans, (b) C. pan, (c) C. p. palmus, (d) C. u. uranus.
Figure 11 – C. t. thysbe 5 in Chrysoritis Butler (Papilionoidea: Lycaenidae: Aphnaeinae) - Part II: Natural history: morphology, ecology, and behaviour, with accounts of larval ecology and insights into the aphytophagous C. dicksoni (Gabriel)
Figure 11 – C. t. thysbe 5th instar plus two Crematogaster peringueyi ants engaged in mutual trophallaxis, sharing honeydew that was taken from the larva's DNO (Blaauwberg N. Res.)
Fig. 8 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 8. Classification tree model computed from the morphometric characters of complete specimen data (with carapace sculpturing). A binary decision is made at each node, where 'true' for the node description lead to branch at left and 'false' to right. Probability of correct prediction ('recall') at each terminal node ('leaf') is also shown.
Fig. 7 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 7. Light and scanning electron micrograph of cyprids of: A, B, Amphibalanus reticulatus; C, OTU 2; D, Amphibalanus amphitrite; and E, OTU 1. Carapace sculpturing were absent in this group of cyprids.
Fig. 9 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 9. Composition of barnacle cyprid diversity at different stations and different year of collection.
Fig. 6 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 6. Light and scanning electron micrograph of cyprids of: A–H, Amphibalanus variegatus; and I–L, Euraphia withersi. Details of specific carapace sculpturing patterns in each species are shown at higher magnification. 6I, E. withersi has reddish pigments around the carapace (arrows) and a dark rounded pigmentation spot (circled).
Fig. 5 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 5. Light and scanning electron micrograph of cyprids of: A–D, Fistulobalanus sp.; and E–J, Fistulobalanus patellaris. Details of specific carapace sculpturing patterns in each species are shown at higher magnification.
Fig. 2 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 2. Lateral view of cyris larvae of barnacle showing measurements used for morphometric analysis. CL: carapace length; CH: carapace height; A: posterior carapace angle. Ratio of CL/CH was also calculated.
Fig. 1 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 1. Map of sampling locations at Matang Mangrove Forest Reserve (MMFR) in Perak, Malaysia. Sampling was carried out in April 2011 at sites 1–8 and in June 2012 at sites 9–14.
Fig. 4 in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 4. Histogram showing variations of pair-wise genetic distances computed from 12S-rRNA gene fragment sequences using Kimura 2-parameter model. Note the distribution of within-species variations does not overlap with that of inter-species variation.
Fig. 3. Neighbour-joining tree contructed from partial 12S in A combined morphological and molecular approach in identifying barnacle cyprids from the Matang Mangrove Forest Reserve in Malaysia: essentials for larval ecology studies
Fig. 3. Neighbour-joining tree contructed from partial 12S-rRNA gene fragment sequences of cyprids and adults of barnacle. The sequences were clustered into eight clades, and species name were labelled at the clades containing sequence(s) of identified adult of barnacle. Clades with no sequence of identified barnacle adult clustered within were designated as OTU (Operational Taxonomic Unit). Number of sequences in each clade were also shown. Scale bar denotes 0.02 base substituition per site.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.