Biological sampling protocol

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Katie Hein

At each river-road node, the biological team sampled fish and shrimp upstream and downstream from the road with a variety of methods. Below, we describe the details of the study design for each method.

At each node, we sampled one to four pools: the pools immediately up and downstream from the road, and a second pool up and downstream from the road within 325 m of the road crossing. If the pool extended below the road crossing, we sampled the entire thing. At low elevations where brackish water reached the road crossing, we only sampled upstream from the road.


  1. Snorkeling: Two people snorkeled one transect each along the length of the pool simultaneously. Each snorkeler held a 1 m long stick in front of and perpendicular to his/her body to demarcate the sampling area. He/she identified and counted the number of each fish species seen while swimming upstream. We only snorkeled when turbidity was low, where sewer water was not entering the stream, and in pools deep enough to swim (> 1 m).

  2. Trapping: We used three types of traps to sample all pools at all sites. Wire mesh gee minnow traps (0.635 cm mesh, 22.9 cm diameter, 44.5 cm long) with a 3.5 cm diameter opening, gee minnow traps with a 5 cm diameter opening, and large cylindrical traps (1.4 X 2.6 cm mesh, 35 cm diameter, 65 cm long) with a 13 cm diameter opening. In small pools (< 30 m2), we set 1 of each type of trap, and we set 3 of each type of minnow trap and 2 large traps in medium pools (30-200 m2). In large pools (> 200 m2), we set 5 of each type of minnow trap and 2 large traps. Each trap was baited with 22 g of cat food and set over night. The traps with larger openings captured large Macrobrachium sp., Agonostomus monticola, Anguilla rostrata, Eleotris pisonis, Epilobocera sinuatifrons, Gobiomorous dormitor, and Sicydium plumieri, whereas minnow traps with a small opening effectively captured Atya sp., Xiphocaris elongata, Anguilla rostrata, and juvenile Macrobrachium sp. A few Eleotris pisonis, Epilobocera sinuatifrons, Gobiomorous dormitor, Poecilia vivipara, and Sycidium plumieri were also captured in minnow traps with a small opening. Each individual was identified to species, but juvenile Macrobrachium could not be identified to species.

  3. Electrofishing: One person used a backpack shocker to stun and net fish, and a second person helped to net fish in each pool and/or associated riffle. The electrofishing team moved upstream, sweeping from one side of the pool to the other until they reached the upper bound of the pool. The team also shocked riffles adjacent to the pools trapped and snorkeled. When the pools were too large to electrofish effectively (> 215 m2, > 1.3 m deep), the team only electrofished the riffles.

** The total number of freshwater fish species found at a site could include (latin, English, Spanish names):

    1. Agonostomus monticola, mountain mullet, dajao

    2. Anguilla rostrata, American eel, anguila

    3. Awaos tajasica, river goby, saga or ciaga

    4. Eleotris pisonis, spinycheek sleeper, moron

    5. Gobiomorus dormitor, bigmouth sleeper, guavina

    6. Poecilia sp.(vivipara?), guppy, sardinita

    7. Sicydium plumieri, sirajo goby, olivo or chupa piedras or setí or tri-tri

All species were native except Poecilia sp. We did not include estuarine fish in our calculations of the total number of fish present at a site.
** The total number of decapod species found at a site could include (latin, English, Spanish names):

    1. Atya innocous, shrimp, gata or guábara or chágara

    2. Atya lanipes, sinous-faced shrimp, guábara

    3. Atya scabra, serrei shrimp, jonga

    4. Epilobocera sinuatifrons, river crab, buruquena

    5. Macrobrachium acanthurus, ?, silgao

    6. Macrobrachium carcinus, giant-hand shrimp, bocú

    7. Macrobrachium crenulatum, pubescent-hand shrimp, camaron

    8. Macrobrachium faustinum, pubescent-hand shrimp, camaron

    9. Macrobrachium heterochirus, teeth-faced shrimp, leopardo

    10. Xiphocaris elongata, glass or long-faced shrimp, salpiche or chiripi or chillo

All species were native.
** Rows by species give the presence or absence of a particular species at each site (0 indicates absence and 1 indicates presence).

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