Phylogenetic and proximate mechanisms affect darter (Percidae: Etheostomatinae) community structure

Understanding the relative influences of biotic and abiotic mechanisms responsible for generating patterns of community diversity remains a fundamental theme in ecology. Although studies have recovered patterns of community structure, the mechanisms responsible for such patterns are often unclear. To better understand assembly mechanisms, I implemented a framework that incorporated phylogeny, morphology, and habitat use data among co-occurring darters (Percidae: Etheostomatinae). Darters are small bodied stream fishes endemic to North America, and due to the high degree of co-occurrence of species in fine scale communities, these systems are ideal for testing assembly mechanisms where inter-specific interactions are plausible. My goals were to identify patterns of habitat use structure, describe mechanisms influential on assembly, and demonstrate the effects of spatial scale on assembly mechanisms within darter communities. To test for mechanisms influential on community assembly, I incorporated metrics of phylogenetic relatedness, habitat use similarity, and morphologic similarity, among co-occurring species within communities at several spatial scales. At the stream site scale, communities showed consistent phylogenetic clustering and habitat use clustering among co-occurring taxa, indicating that habitat filtering (i.e., co-occurrence of species with similar ecological requirements) was the main driver of community assembly; although some degree of evolutionary convergence in habitat use among co-occurring species was found. There were separations in habitat use but these occurred between groups of species rather than among all individual species. Additionally, phylogenetic/habitat use relationships indicated displacement in habitat use among recently diverged taxa. Across multiple spatial scales (from within to across four watersheds) darter communities showed an increase in the prevalence of habitat filtering from fine to intermediate spatial scales, and in two of the four systems there was a signal for habitat filtering at the most broad scale. There was a strong signal for competitive exclusion in only one of the river systems. In conclusion, darter communities showed group separation in habitat use, where similar habitat use is found within groups of species suggesting that competition may not act strongly among individual species within these communities, but rather, competition could act between species groups. Habitat filtering appeared to be the dominate mechanism influencing the assembly of communities, and the relative influence of habitat filtering increased with larger spatial scales. However, the prevalence of simultaneous signal for habitat filtering and competitive exclusion based on trait distributions and phylogenetic patterns further illustrates the complexities of community assembly processes

Objectively measuring subjectively described traits: Geographic variation in body shape and caudal coloration pattern within vieja melanura (Teleostei: Cichlidae)

© 2017, Universidad de Costa Rica. All rights reserved. Vieja melanura is a Neotropical cichlid occurring in the Petén-lake district systems of Guatemala, as well as the Río Grijalva-Usumacinta basin, and other systems in Southern México, Belize, and Guatemala. A caudal stripe, extending forward from the caudal peduncle, is characteristic of this species. This stripe is sloped downward in nearly all individuals of V. melanura, but the degree of the slope is highly variable throughout its range. The slope and shape of the stripe has previously been used in diagnosing and differentiating between species of Vieja. The purpose of this study was to use objective methods to investigate morphological variation in the caudal stripe and body shape throughout the range of V. melanura. We studied geometric morphometric analyses of body shape and empirical measurements of the slope of the caudal stripe in 215 specimens of V. melanura. We also used the mitochondrial cytochrome b marker to study population level patterns within V. melanura. Results from our analyses showed significant geographic variation in body shape and patterns of coloration with little mitochondrial phylogeographic structure. These patterns likely correspond to differences in riverine habitats throughout the species’ distribution. In conclusion, these results can be used to inform other studies of color and shape variation as it applies to taxonomy and systematics

Additions to Philippine Slender Skinks of the <i>Brachymeles bonitae </i>Complex (Reptilia: Squamata: Scincidae) III:a new species from Tablas Island

Davis, Drew R., Geheber, Aaron D., Watters, Jessa L., Penrod, Michelle L., Feller, Kathryn D., Ashford, Alissa, Kouri, Josh, Nguyen, Daniel, Shauberger, Kathryn, Sheatsley, Kyra, Winfrey, Claire, Wong, Rachel, Sanguila, Marites B., Brown, Rafe M., Siler, Cameron D. (2016): Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) III: a new species from Tablas Island. Zootaxa 4132 (1), DOI: http://doi.org/10.11646/zootaxa.4132.1.

Additions to Philippine Slender Skinks of the <i>Brachymeles bonitae </i>Complex (Reptilia: Squamata: Scincidae) I:a new species from Lubang Island

Geheber, Aaron D., Davis, Drew R., Watters, Jessa L., Penrod, Michelle L., Feller, Kathryn D., Davey, Conner S., Ellsworth, Elyse D., Flanagan, Rachel L., Heitz, Brendan B., Moore, Tana, Nguyen, Marie D. C., Roberts, Austyn, Sutton, John, Sanguila, Marites B., Linkem, Charles W., Brown, Rafe M., Siler, Cameron D. (2016): Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) I: a new species from Lubang Island. Zootaxa 4132 (1): 1-14, DOI: http://doi.org/10.11646/zootaxa.4132.1.

Paraneetroplus melanurus Gunther 1862

Re-description of Paraneetroplus melanurus (Günther 1862) Lectotype. BMNH 1864.1. 26.82 (Fig. 7). Type locality is Lake Petén, Guatemala. We designate the largest syntype as the lectotype and the remaining four specimens as paralectotypes (BMNH.1864.1.26.78- 81). Synonyms. Heros melanurus Günther 1862, Heros melanopogon Steindachner 1864, Cichlasoma synspilum Hubbs 1935, Cichlaurus hicklingi Fowler 1956 Material examined. Paraneetroplus melanurus — GUATEMALA: UMMZ 143888 (n= 11), 143889 (n= 2), 143937 (n= 30), 143940 (n= 30), 143949 (n= 3), 187210 (n= 4); BMNH 1864.1.26.78- 82 (n= 5) [Lago de Petén]; UMMZ 95518 (n= 1) [Río San Pedro de Mártir; Río Usumacinta Drainage]; UMMZ 189985 (n= 23) [Río Chixoy]; UMMZ 144044 (n= 17) [Laguna Perdida]; UMMZ 144035 (n= 7) [Laguna de Eckibix]; UMMZ 144048 (n= 18) [Laguna de Yalac]; UMMZ 144053 (n= 18) [Río de la Pasión; Río Usumacinta Drainage]. MEXICO: UMMZ 196488 (n= 2), 210868 (n= 5) [Laguna Bacalar]; UMMZ 184628 (n= 7), 184637 (n= 2) [Río Chilapa; Río Grijalva Drainage]; UMMZ 196435 (n= 30) [Río Usumacinta]; UMMZ 196605 (n= 11) [Gulf of Campeche]; UMMZ 210943 (n= 2) [Río El Huil; Río Usumacinta Drainage]. BELIZE: UMMZ 167692 (n= 1), 190144 (n= 1), 190149 (n= 1), 202885 (n= 22) [Río Belize]. COMPARATIVE MATERIAL— P. maculicauda (UMMZ 180667, n= 3, Costa Rica: Tortugero; UMMZ 195944; n= 1; Belize: Golden Stream); P. guttulatus (UMMZ 194116, n= 5, Guatemala: Río Sis); P. z o n a t u s (UMMZ 178573, n= 4, Mexico: Río Tehuantepec); P. fenestratus (SLU 5022; n= 1; Río Chiquito); P. argentea (UMMZ 189984; n= 4; Guatemala: Río Chixoy); P. regani (UMMZ 184757; n= 2; Mexico: Río Coatzacoalcos); P. bulleri (BMNH 90.10. 10.94, n= 1, Mexico: Río de Sarabia; FMNH 63937, n= 1, Mexico: Río Papaloapan); P. hartwegi (UMMZ 186407, n= 3, Mexico: Río Grijalva); P. breidohri (UMMZ 193906, n= 3, Guatemala: Río Usumacinta); P. bifasciatus (UMMZ 143879, n= 2, Guatemala: Río Usumacinta). Diagnosis. Paraneetroplus melanurus possesses a single dark horizontal to slightly angled band or stripe that typically extends from the caudal-fin base to near the mid-point of the body; ranging from about one-third to nearly half the length of the body. The band appears as a series of connected dark blotches that, in many specimens, are then broken into separated blotches near the band’s anterior extent (Figs. 6, 7, and 8 b). The characteristic “caudal band” is present in both adults and large juveniles, and distinguishes the species from its congeners as well as all other syntopic cichlid fishes. This species is most closely related to Paraneetroplus maculicauda (Hubbs 1935; McMahan et al. 2010) which occurs from the Río Usumacinta drainage south to the Río Chagres in Panama (Kullander 2003). Paraneetroplus melanurus is clearly distinguished from P. maculicauda by the presence in P. melanurus of a long black caudal band, often extending to mid-body. In P. maculicauda, the “band” is absent, replaced by a single large dark blotch at the caudal-fin base (Fig. 8 a). In addition, adult P. maculicauda typically possess a dark vertical bar (belt) at midbody (Fig. 8 a). This character is absent in P. melanurus. The caudal band of P. melanurus also allows this species to be differentiated from all other members of the genus Paraneetroplus (sensu McMahan et al. 2010). In contrast to P. melanurus, the three congeners P. guttulatus, P. zonatus, and P. fenestratus each have a longitudinal band that extends the entire length of the body. Paraneetroplus argentea and P. regani are distinguished from P. melanurus by the absence of a caudal band. Paraneetroplus bulleri is distinguished from P. melanurus based on the presence in P. bulleri of an irregular longitudinal stripe down the body that ends at or just before the caudal-fin base and includes a series of large dark blotches. Paraneetroplus bulleri also possesses a prominent rounded snout (versus angular in P. melanurus) and a more elongate body. Paraneetroplus hartwegi can be distinguished from P. melanurus by the presence of lateral blotches/bars that form a nearly complete longitudinal stripe down the body, which begins with a blotch dorsal to the pectoral fin. Paraneetroplus bifasciatus differs from P. melanurus based on the presence of two stripes along each side of the body. The upper stripe may be a blotch if not developed; however, the lower stripe runs from the pectoral fin base to the caudal fin. Paraneetroplus breidohri differs from P. melanurus by possession of a relatively complete longitudinal dark band extending from near the head to the caudal-fin base. Description. Morphometric data on the lectotype and paralectotypes are reported in Table 3. Paraneetroplus melanurus possesses the following set of meristic traits: average dorsal fin formula XVII 12 [range XV–XVIII 10– 15], anal fin formula VI 9 [range V–VII 7–11], upper lateral-line scales usually 20-22 (range 16–24); lower lateralline scales usually 11–14 (range 7–16); 2 (rarely 1) scale rows between upper and lower lateral line. Individuals possess deep oval shaped bodies (42.8 % SL in type material) and consistently have a prominent black caudal band. The band is variable, either blotched (discontinuous) or mostly solid (i.e. non-blotched), typically becoming more broken anteriorly. Slope of the caudal band is somewhat variable, ranging from nearly straight and horizontal in orientation to slightly angled, ventrally sloping anteriorly. The slope and blotched pattern of the caudal band may differ between left versus right side of the body of the same individual (Fig. 6). Small juveniles may possess a relatively straight caudal band; however, large juveniles and adults typically possess downward sloped bands. Most specimens possess a series of dark blotches along the dorso-lateral scales ventral to the dorsal fin. Breeding males of this species possess a large nuchal hump (Fig. 7). Lectotype Range Mean SD Standard length (mm) 207.0 63.2 –207.0 Coloration in alcohol. Body with an overall brown color; smaller individuals may be a darker brown. Caudal band and dorso-lateral blotches remain black or dark. Dorsal, anal, pelvic, and caudal fins tan, with juveniles often possessing dark spots on fins. Pectoral fins are translucent and relatively colorless in adults, but occasionally having dark spots. Coloration in life. Live specimens have an overall dusky tone, with a gray to yellowish body (Fig. 9). The caudal band and dorso-lateral blotches are black or dark. Fins are a dusky color, often having small dark spots. Individuals may have areas of blue, green, or yellow scales on the body. Adults in breeding condition typically have extensive red or pink on the breast area and sometimes extending over much of the anterior part of the body, with such variation possibly related to localized differences across the native range (Conkel 1997, Schmitter-Soto 1998). Breeding individuals also display blue and yellow coloration on fins. Etymology. While not stated in Günther’s original description, the specific epithet appears to be derived from the Greek melanos (black) and oura (tail), likely in reference to the characteristic caudal band of this species. Description of Lectotype. The lectotype is the largest of the five original syntypes (Fig. 7). The specimen appears well preserved and still possesses distinguishable markings. It is an adult male of 207 mm SL, 55.08 mm from posterior of orbit to pectoral fin, 53.07 mm from posterior of dorsal to anal fin, 88.75 mm from anterior of dorsal to pelvic fin, and 11.13 mm orbit diameter. Dorsal fin XVII 12, anal fin VI 8, 14 pectoral rays, 22 upper lateral-line scales, 13 lower lateral-line scales, 7 scale rows from anal fin to lower lateral line, 2 scale rows between upper and lower lateral line, 6 scales from pectoral to pelvic fin. The gill rakers are relatively short and conical. The maxillary cleft is ventral to the dorsal margin of the pectoral-fin base, and the upper and lower jaws do not extend one over the other. The left side of the specimen possesses a ventral-sloped caudal band, ending anteriorly ventral to the lower lateral line. The caudal band on the right side of the specimen is incomplete, consisting of moderately defined blotches; however, this band also continues to ventral the lower lateral line. The lower lateral line runs through the center of the posterior portion of the caudal band. On both sides of the specimen a series of 3–4 joined dorso-lateral blotches is present. Teeth are conical. The lectotype possesses a nuchal hump on the head, characteristic of breeding males of this species. Intraspecific variation. Variation in meristic characters is minimal throughout the range of this species. Most variation is associated with the pattern and slope of the caudal band, and this variation does not appear to be geographically differentiated. There is also variation in color pattern (see section on coloration, above). Distribution. Paraneetroplus melanurus naturally occurs along the Atlantic slope in the Río Grijalva-Usumacinta system, and east and southward throughout Quintana Roo, Mexico, and Belize to the Lago de Petén system of Guatemala. An introduced population is presumably established in Singapore (Ng and Tan 2010), and the specimens, likely released pet fish, have been reported for open waters of the USA (Fuller et al. 1999) and the Philippines (Froese and Pauly 2009).Published as part of Mcmahan, Caleb D., Murray, Christopher M., Geheber, Aaron D., Boeckman, Christopher D. & Piller, Kyle R., 2011, Paraneetroplus synspilus is a Junior Synonym of Paraneetroplus melanurus (Teleostei: Cichlidae), pp. 1-14 in Zootaxa 2833 on pages 10-13, DOI: 10.5281/zenodo.20755

Putting eDNA to the Test: A Field Comparison of eDNA Metabarcoding to Established Protocols for Assessing Biodiversity in Missouri’s Ozark Highland Streams

Aquatic biodiversity monitoring to inform conservation and management efforts in stream systems has increasingly begun to incorporate eDNA-based sampling methods. We conducted a comparison of eDNA metabarcoding to a traditional protocol of combined seining and electrofishing methods to assess fish biodiversity of wadeable stream sites in six separate drainages in the Ozark Highlands of Missouri. The study further focused on the headwaters of the Meramec River, which included eleven sites and seasonal sampling (summer and winter). We compared estimates of diversity across sampling methods, assessed hypothesized relationships of habitat (depth and velocity) and season (summer vs winter) to eDNA detection, and tested the effects of sampling method and site locality on fish assemblage structural dynamics. eDNA sampling detected approximately double the number of species detected compared to traditional methods, providing higher diversity estimates while maintaining the relative ranking of sites. eDNA detection probabilities were positively associated with stream depth and velocity and were generally higher in summer than in winter but not for all species. Assemblage differences between tributary and mainstem sites were attributable to a small number of species that were found predominantly in one stream size category or the other, indicating that eDNA was sensitive to within-drainage assemblage structure relationships. Improved species detection and a more comprehensive understanding of assemblage structural dynamics are important benefits encouraging the use of eDNA metabarcoding as a primary collection method in future stream biodiversity assessment and monitoring programs

Putting eDNA to the test: A field comparison of eDNA metabarcoding to established protocols for assessing biodiversity in Missouri's Ozark Highland streams

AbstractAquatic biodiversity monitoring to inform conservation and management efforts in‐stream systems has increasingly begun to incorporate environmental DNA (eDNA)‐based sampling methods. We conducted a comparison of eDNA metabarcoding to a traditional protocol of combined seining and electrofishing methods to assess fish biodiversity of wadeable stream sites in six separate drainages in the Ozark Highlands of Missouri (USA). The study further focused on the headwaters of the Meramec River, which included 11 sites and seasonal sampling (summer and winter). We compared estimates of diversity across sampling methods, assessed the influences of water flow (depth, velocity, and discharge) and season, and tested the effects of sampling method and site locality on fish assemblage composition. eDNA sampling detected approximately double the number of species compared to traditional methods, providing higher diversity estimates while maintaining the relative ranking of sites. eDNA detection probabilities were positively associated with stream depth and velocity and were generally higher in summer than in winter but not for all species. Estimated species richness was positively associated with discharge for both methods but the relationship was stronger with eDNA sampling. Assemblage differences between tributary and mainstem sites were attributable to a small number of species that were found predominantly in one stream size category or the other, indicating that eDNA was sensitive to within‐drainage assemblage structure relationships. We highlight improved species detection, a more comprehensive understanding of assemblage structural dynamics, and the potential ability to integrate data across sampling methods as important benefits that encourage the use of eDNA metabarcoding as a primary collection method in future stream biodiversity assessment and monitoring programs

FIGURE 3 in Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) III: a new species from Tablas Island

FIGURE 3. Photograph of lateral and ventral views of head of preserved holotype of Brachymeles dalawangdaliri sp. nov. (CAS 137149). Photographs taken by JLW and MLP.Published as part of Davis, Drew R., Geheber, Aaron D., Watters, Jessa L., Penrod, Michelle L., Feller, Kathryn D., Ashford, Alissa, Kouri, Josh, Nguyen, Daniel, Shauberger, Kathryn, Sheatsley, Kyra, Winfrey, Claire, Wong, Rachel, Sanguila, Marites B., Brown, Rafe M. & Siler, Cameron D., 2016, Zootaxa 4132 (1), DOI: 10.11646/zootaxa.4132.1.3, http://zenodo.org/record/25893

FIGURE 2 in Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) II: a new species from the northern Philippines

FIGURE 2. Illustration of head of Brachymeles ilocandia sp. nov. (PNM 9819, holotype) in dorsal, lateral, and ventral views. Taxonomically diagnostic head scales are labeled as follows: C, chin shield; F, frontal; FN, frontonasal; FP, frontoparietal; IL, infralabial; IP, interparietal; L, loreal; M, mental; N, nasal; Nu, nuchal; P, parietal; PF, prefrontal; PM, postmental; PO, preocular; PSO, presubocular; R, rostral; SC, supraciliary; SL, supralabial; SN, supranasal; and SO, supraocular. Roman numerals indicate scales in the supraocular series, with Arabic numbers indicating scales in the supraciliary series. Illustrations by MLP and CDS.Published as part of Siler, Cameron D., Davis, Drew R., Freitas, Elyse S., Huron, Nicholas A., Geheber, Aaron D., Watters, Jessa L., Penrod, Michelle L., Papeș, Monica, Amrein, Andrew, Anwar, Alyssa, Cooper, Dontae, Hein, Tucker, Manning, Annalisa, Patel, Neeral, Pinaroc, Lauren, Diesmos, Arvin C., Diesmos, Mae L., Oliveros, Carl H. & Brown, Rafe M., 2016, Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) II: a new species from the northern Philippines, pp. 15-29 in Zootaxa 4132 (1) on page 20, DOI: 10.11646/zootaxa.4132.1.2, http://zenodo.org/record/26674