First Molecular Verification of a Marine-collected Specimen
of Alosa alabamae (Teleostei: Clupeidae)
Paul F. Mickle, Jim S. Franks, Brian R. Kreiser, Gary J. Gray, Jeremy M. Higgs, and Jeanne-Marie Havrylkoff
Southeastern Naturalist, Volume 14, Issue 3 (2015): 596–601
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Southeastern Naturalist
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2015 Vol. 14, No. 3
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2015 SOUTHEASTERN NATURALIST 14(3):596–601
First Molecular Verification of a Marine-collected Specimen
of Alosa alabamae (Teleostei: Clupeidae)
Paul F. Mickle1,*, Jim S. Franks2, Brian R. Kreiser4, Gary J. Gray2,
Jeremy M. Higgs2, and Jeanne-Marie Havrylkoff
4
Abstract - Alosa alabamae (Alabama Shad) is an imperiled anadromous species
that reproduces in northern Gulf of Mexico drainages. To date, there have only been
4 vouchered specimens collected from marine waters, but none have been verified
with molecular techniques. On 28 March 2013, we collected a single adult female in
proximity to a barrier island (Petit Bois) off the coast of Mississippi. Microsatellite
DNA analysis corroborated the identification of this individual and suggested that
the specimen was most genetically similar to the group from the Pascagoula River
drainage rather than other portions of the range. Thus far, research has been focused
on the species’ freshwater life history, and it is crucial that more effort be directed
toward documenting and understanding the full life history of t his threatened fish.
Introduction
Alosa alabamae Jordan and Evermann (Alabama Shad) is an anadromous fish
that has a federal status of special concern, is listed as endangered by some states,
and has been extirpated from many drainages throughout its range (Meadows et al.
2006, NOAA 2015). Adults migrate from marine habitats into natal rivers to spawn
during spring months (February–May) before returning to the Gulf of Mexico
(GOM; Mettee and O’Neil 2003). The species’ distribution ranges from Missouri to
Florida, but no published information is available about its marine distribution in the
GOM. Only 4 Alabama Shad (Fishnet catalog numbers: 293755.5174309, 28671,
20627[2]) have ever been recorded in collections within the marine environment
outside the boundaries of an estuary (Alabama and Florida; Fishnet2 2015). Past
research of Alabama Shad was limited to riverine habitats and focused on aspects
of juvenile and adult life history such as habitat use, diet, and spawning (Ely et al.
2008; Mettee and O’Neil 2003; Mickle et al. 2010, 2013). There is clearly a need
for studies focused on the adult life stage in marine and estuarine environments. In
this paper, we report the first molecularly verified record of an adult Alabama Shad
from marine waters, thereby providing a glimpse into one important aspect of this
species’ life history.
1The Mississippi Department of Marine Resources, 1141 Bayview Avenue, Biloxi, MS
39530. 2The University of Southern Mississippi, Center for Fisheries Research and Development,
Ocean Springs, MS 39564. 3Department of Coastal Science, Gulf Coast Research
Laboratory, 703 East Beach Drive Ocean Springs, MS 39564. 4The University of Southern
Mississippi, Department of Biological Sciences, 118 College Drive # 5018, Hattiesburg, MS
39406-5018. *Corresponding author - paul.mickle@dmr.ms.gov.
Manuscript Editor: Hayden T. Mattingly
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Materials and Methods
We captured a single adult Alabama Shad on 28 March 2013 within the statedesignated
marine waters of Mississippi (Fig. 1). We collected the specimen just
north of Petit Bois Island and 4.8 km east of Horn Island Pass, which leads to the
open GOM (Table 1). We obtained the fish during a fishery independent monitoring
project (Mississippi Coast Sport Fish Study, conducted by The University of
Southern Mississippi - Gulf Coast Research Laboratory) in a 11.43-cm mesh panel
of a 182.88-m experimental multi-paneled gill net that was soaked for 136 min. We
measured (total length [TL]), weighed (total weight [TW]), sampled (fin tissue) for
genetic analysis, and deposited the specimen in the Mississippi Museum of Natural
Science, Jackson, MS, Lot #61556.
Some clupeid species are morphologically and meristically similar, thus, we
conducted a microsatellite-DNA analysis to confirm species identification and
assign the individual to a natal drainage. The molecular analysis was based on a
reference collection of 473 Alabama Shad from 6 drainages—the Gasconade, Little
Missouri, Ouachita, Pascagoula, Choctawhatchee, and Apalachicola rivers. This
reference collection is the basis of an unpublished study of range-wide population
structure (Bowen 2005). Genotyping the adult individual in our study was
performed in the same laboratory and using the same methods as Bowen (2005).
Briefly, the following methods were used. We genotyped individuals using the polymerase
chain reaction (PCR) to amplify 16 microsatellite loci (Аѕа-2, Аѕа-4, Аѕа-9,
Аѕа-16 [Waters et al. 2000]; Аа14, Аа16, Аа20 [Faria et al. 2004]; and AsaB020,
AsaC249, AsaC334, AsaD021, AsaD030, AsaD055, AsaD312, AsaD392, AsaD492
[Julian and Barton 2007]) in a total volume of 12.5 μl using 1X reaction buffer
(Promega Company, Madision, WI), 1.5–3.0 μM MgCl2, 200 μM dNTPs, 0.4 units
of Taq polymerase (Promega Company), 0.3 μM of the M13 tailed forward primer
(Boutin-Ganache et al. 2001), 0.3 μM of the reverse primer, 0.1 μM of the labeled
M13 primer, 20–150 ng of template DNA, and water to the final volume. PCR cycling
conditions consisted of an initial denaturing step at 94 °C for 2 min followed
by 35 cycles of 30 sec at 94 °C, 1 min at 50–61 °C, and 1 min at 72 °C. A final
elongation step of 10 min at 72 °C ended the cycle. We visualized microsatellite
alleles on acrylamide gels using a LI-COR 4200 automated DNA sequencer (LICOR,
Lincoln, NE), and scored allele sizes using GENE IMAGIR v 3.55 software
(LI-COR).
We conducted tests for Hardy-Weinburg equilibrium (HWE) and linkage
disequilibrium (LD) using GENEPOP for the web (http://genepop.curtin.edu.
au/; Raymond and Rousset 1995) and measured genetic variation by the number
of alleles, observed heterozygosity (Ho), and expected heterozygosity (He) as
calculated by GenAlex 6.501 (Peakall and Smouse 2006). We employed MICROCHECKER
v. 2.2.3 (van Oosterhout et al. 2004) to detect the presence of null
alleles and FSTAT 2.9.3 (Goudet 1995) to calculate Weir and Cockerham’s (1984)
unbiased estimator of FST. Bowen (2005) suggested that there are 3 genetically
discrete populations (K) represented by the data as estimated using STRUCTURE
2.3.3 (Pritchard et al. 2000). To assign our adult specimen to 1 of the genetic
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groups defined by STRUCTURE, we performed another analysis following the
recommendations for the USEPOPINFO model found in the STRUCTURE manual.
We used individuals from the Apalachicola (n = 201), Pascagoula (n = 188),
and Mississippi (n = 76) river basins as representatives of the 3 genetic groups
where individuals had average membership coefficients (q scores) >0.95. Parameters
for this analysis included 20 independent runs with a burn-in of 250,000
followed by 500,000 MCMC replications.
Results
The specimen was 383 mm TL, 710 g TW, and female with visually observed,
well-developed ovaries (Fig. 1). The stomach was filled with what appeared to be
Figure 1. Image of the collected adult female Alabama Shad (A). Image of the specimen’s
well-developed ovaries (B).
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2015 Vol. 14, No. 3
small invertebrates. Physiochemical (water quality) data taken at the collection site
were typical (Jewel et al. 2015) for the marine zone from which the specimen was
collected (Table 1).
In the reference populations, none of the loci consistently deviated from HWE
expectations or demonstrated LD, and we did not detect null alleles. The average
number of alleles across loci at a site ranged from 3.2 to 8.1, while average Ho and
He were 0.40–0.49 and 0.37–0.48, respectively. Pairwise FST values were smallest
between the Choctawhatchee and Apalachicola drainages (0.006), and the largest
values occurred between the Mississippi River drainages and the GOM drainages
(0.092–0.119). The average q score of this specimen was 0.82 (SD = 0.06) in the
Pascagoula group.
Discussion
This species is anadromous, and considering the collection date, it is likely the
animal was preparing for a spawning run within one of the proximate rivers. The
mouth of the Pascagoula River is 14.8 km north of the collection site, and this particular
drainage has shown past recruitment for Alabama Shad (Mickle et al. 2010,
Ross 2003). Mills (1972) and others have reported few to no diet items from adults
collected in riverine habitats. As with numerous other anadromous fishes, Alabama
Shad most likely feeds primarily in marine habitats, which supports the need for
marine research of this species (Mettee and O’Neil 2003).
Despite the existence of the FishNet collections mentioned above, it remains
largely unknown what marine regions are utilized by adult Alabama Shad.
The similar appearance of this species to Brevoortia patronus Goode (Gulf
Menhaden) has probably contributed to misidentification and lack of reported
occurrences from marine environments. With the majority of North American
anadromous fishes in decline, research on these species, including Alabama
Shad, must include life histories, environmental requirements, and migratory demands
(Limburg and Waldman 2009). Projected increasing human populations in
the northern GOM states will most likely produce additional anthropogenic pressures
on the natal drainages that support anadromous fishes (US Census 2015).
Considering the imperiled status of Alabama Shad, it is essential that the ecology
and all life-history aspects of this species are documented for its riverine, estuarine,
and marine habitats.
Table 1. Physiochemical data recorded during collection of the specimen of Alabama Shad from location
30.22797ºN, 88.45806ºW.
Parameter Surface Bottom
Water temperature 14.9 ºC 15.1 ºC
Salinity 21.8 ppt 23.4 ppt
Dissolved oxygen 9.19 mg/L 8.87 mg/L
Water depth 4.3 m
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Acknowledgments
The specimen was collected during a Gulf Coast Research Laboratory (GCRL) fisheries
project funded by the US Fish and Wildlife Service, Sport Fish Restoration Program, and
the Mississippi Department of Marine Resources. We thank The University of Southern
Mississippi’s Department of Coastal Sciences and Center for Fisheries Research and Development
for vessel and personnel support.
Literature Cited
Boutin-Ganache I., M. Raposo, M. Raymond, and M. Deschepper. 2001. M-13 tailed primers
improve the readability and usability of microsatellite analyses performed with two
different allele-sizing methods. BioTechniques 31:24–28.
Bowen, B.R. 2005. Alabama Shad phylogeography. M.Sc. Thesis. The University of Southern
Mississippi, Hattiesburg, MS.
Ely, P.C., S.P. Young, and J.J. Isley. 2008. Population size and relative abundance of adult
Alabama Shad reaching Jim Woodruff Lock and Dam, Apalachicola River, Florida.
North American Journal of Fisheries Management 28:827–831.
Faria, R., B. Wallner, S. Weiss, and P. Alexandrino. 2004. Isolation and characterization of
eight dinucleotide microsatellite loci from two closely related clupeid species (Alosa
alosa and A. fallax). Molecular Ecology Notes 4:586–588.
Fishnet2. 2015. Alabama Shad historical collection data in the Gulf of Mexico: 1957–2014.
Available online at http://www.fishnet2.net. Accessed 4 January 2015.
Goudet, J. 1995. FSTAT version 1.2: A computer program to calculate F-statistics. Journal
of Heredity 86:485–486.
Limburg, K.E., and J.R. Waldman. 2009. Dramatic declines in north Atlantic diadromous
fishes. BioScience 59:955–965.
Jewell, J., M.T. Hill, and M.K. Brainard. 2015. Monitoring and assessment of Mississippi’s
interjurisdictional marine resources. Technical report. Mississippi Department of Marine
Resources, Biloxi, MS. 12 pp.
Julian, S.E., and M.L. Barton. 2007. Microsatellite DNA markers for American Shad (Alosa
sapidissima) and cross-species amplification within the family Clupeidae. Molecular
Ecology Notes 7:805–807.
Meadows, D.W., S.B. Adams, and J.F. Schaefer. 2006. Threatened fishes of the world: Alosa
alabamae (Jordan and Evermann, 1896) (Clupeidae). Environmental Biology of Fishes
82:173–174.
Mettee, M.F., and P.E. O’Neil. 2003. Status of Alabama Shad and Skipjack Herring in Gulf
of Mexico drainages. Pp. 157–170, In K. Limburg and J. Waldman (Eds.). Biodiversity,
Status, and Conservation of the World’s Shads. American Fisheries Society, Symposium
35, Bethesda, MD.
Mickle, P.F., J.F. Schaefer, S.B. Adams, and B.R. Kreiser. 2010. Habitat use of age 0
Alabama Shad in the Pascagoula River drainage, USA. Ecology Of Freshwater Fish
19:107–115.
Mickle, P.F., J.F. Schaefer, D.A. Yee, and S.B. Adams. 2013. Diet of juvenile Alabama Shad
(Alosa alabamae) in two northern Gulf of Mexico drainages. Southeastern Naturalist
12:233–237.
Mills, J.G. 1972. Biology of Alabama Shad in northwest Florida. Florida Department of
Natural Resources Technical Series 68:24–33.
Southeastern Naturalist
601
P.F. Mickle, J.S. Franks, B.R. Kreiser, G.J. Gray, J.M. Higgs, and J.-M. Havrylkoff
2015 Vol. 14, No. 3
National Oceanic and Atmospheric Administration (NOAA). 2015. Species of concern. Available
online at http://www.nmfs.noaa.gov/pr/species/concern. Accessed 15 April 2015.
Peakall, R., and P.E. Smouse. 2006. GENALEX 6: Genetic analysis in Excel. Population
genetic software for teaching and research. Molecular Ecology Notes 6:288–295.
Pritchard, J.K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using
multilocus genotype data. Genetics 155:945–959.
Raymond, M., and F. Rousett. 1995. GENEPOP (version 1.2): Population-genetics software
for exact tests and ecumenicism. Journal of Heredity 86:248–249.
Ross, S.T. 2003. Inland Fishes of Mississippi. University Press of Mississippi, Jackson,
MS. 624 pp.
US Census. 2015. Available online at http://www.census.gov/quickfacts. Accessed 15
April 2015.
van Oosterhout, C.V., W.F. Hutchinson, D.P.M.Wills, and P. Shipley. 2004. MICROCHECKER:
Software for identifying and correcting genotyping errors in microsatellite
data. Molecular Ecology 4:535–538.
Waters, J.M., J.M. Epifanio, T. Gunter, and B.L. Brown. 2000. Homing behavior facilitates
subtle genetic differentiation among river populations of Alosa sapidissima: Microsatellites
and mtDNA. Journal of Fish Biology 56:622–636.
Weir, B.S., and C.C. Cockerham. 1984. Estimating F-statistics for the analysis of population
structure. Evolution 38:1358–1370.