Historical population demography of red snapper (Lutjanus campechanus) from the northern Gulf of Mexico based on analysis of sequences of mitochondrial DNA

We evaluated stock structure and demographic (population) history of red snapper (Lutjanus campechanus) in the northern Gulf of Mexico (Gulf) via analysis of mitochondrial (mt)DNA sequences from 360 individuals sampled from four cohorts (year classes) at three localities across the northern Gulf. Exact tests of genetic homogeneity and analysis of molecular variance both among cohorts within localities and among localities were non-significant. Nested clade analysis provided evidence of different temporal episodes of both range expansion and restricted gene flow due to isolation by distance. A mismatch distribution of pairwise differences among mtDNA haplotypes and a maximum-likelihood coalescence analysis indicated a population expansion phase that dated to the Pleistocene and probably represents (re)colonization of the continental shelf following glacial retreat. The spatial distribution of red snapper in the northern Gulf appears to have a complex history that likely reflects glacial advance/retreat, habitat availability and suitability, and hydrology. Habitat availability/suitability and hydrology may partially restrict gene flow among present-day red snapper in the northern Gulf and give rise to a metapopulation structure with variable demographic connectivity. This type of population structure may be difficult to detect with commonly used, selectively neutral genetic markers. Introduction The Gulf red snapper (Lutjanus campechanus) is a highly exploited marine fish found primarily along the continental shelf of the Gulf of Mexico (Hoese and Moore 1977; Allen 1985) and subjected to both recreational and commercial fishing (Goodyear and Phares 1990). Red snapper abundance in the northern Gulf of Mexico (Gulf) has decreased by almost 90% since the 1970s (Goodyear and Phares 1990), leading to intensive management beginning in the early 1990s (Christman 1997). A central question regarding conservation and management of red snapper resources in the northern Gulf is whether multiple management units (stocks) exist within the fishery. The question is of importance because separate management of regional stocks, should they exist, is necessary to avoid regional over-exploitation and maintain potentially adaptive genetic variation (Carvalho and Hauser 1995; Hauser and Ward 1998). Prior genetic studies on adult red snapper sampled across the northern Gulf have generally revealed homogeneity among localities, consistent with the existence of a single stock (Camper et al. 1993; Gold et al. 1997; 2001; Garber et al. 2004; but see Bortone and Chapman 1995). The genetic data, however, are not fully consistent with studies of post-juvenile life history and with most tag-and-recapture experiments that indicate adult red snapper are sedentary and exhibit high site fidelity (Fable 1980; Szedlmayer and Shipp 1994; Szedlmayer 1997; but see Patterson et al. 2001). Two hypotheses forwarded to account for these seemingly disparate observations are (1) gene flow, perhaps occurring from hydrodynamic transport of pelagic eggs and larvae across the northern Gulf (Goodyear 1995), is sufficient to preclude genetic divergence, or (2) gene flow across the northern Gulf is limited but there has been insufficient time for semi-isolated lineages to completely sort into monophyletic assemblages (Gold and Richardson 1998; Gold et al. 2001). A third hypothesis is (3) that gene flow/isolation among assemblages or lineages Communicated by P.W. Sammarco, Chauvin C. L. Pruett Æ E. Saillant Æ J. R. Gold (&) Center for Biosystematics and Biodiversity, Department of Wildlife and Fisheries Sciences, Texas A&M University, TAMU 2258, College Station, TX 77843-2258, USA E-mail: [email protected] Fax: +1-979-8454096 Marine Biology (2005) 147: 593–602 DOI 10.1007/s00227-005-1615-8 of Gulf red snapper is a dynamic process that varies in intensity and duration through both time and space. Under this hypothesis, gene flow over the short term could be fairly restricted geographically, while over the long term be more extensive and largely a function of passive and more-or-less random (in terms of strength and duration) movement of individuals at one of any life-history stages. Different assemblages (stocks) might thus arise in the short term but appear homogeneous over the long term. Distinguishing among these hypotheses is problematic in that only the hypothesis of ‘gene flow’ can be falsified rigorously with genetic data and deployment of allele (or genotype) distribution-based statistical tests. This is especially true if gene flow varies in intensity and duration and is demographically insignificant in the short term but sufficient in the long term to preclude genetic divergence. We sought to evaluate these hypotheses, especially the latter, by using a nested phylogeographic (clade) analysis (Templeton 1998) of mitochondrial (mt)DNA sequences. The nested clade approach utilizes evolutionary genealogical information to evaluate the spatial and temporal distribution of genetic variation and often can detect cryptic geographical associations or patterns that are not readily identifiable using traditional population genetic measures. Nested clade analysis can also discriminate between the effects of restricted but recurrent gene flow and historical events such as range expansion and/or population fragmentation (Templeton et al. 1995; Templeton 1998). In addition, we employed both mismatch-distribution analysis and a maximum-likelihood coalescence analysis of mtDNA sequences to further evaluate historical population demography of red snapper in the northern Gulf. Materials and methods A total of 30 individual red snapper from each of four cohorts (year classes) were sampled at each of three localities (Fig. 1) in the northern Gulf of Mexico (n=120 per locality; 360 total). Adult individuals belonging to the 1995 and 1997 cohorts were sampled between 1999 and 2001 by angling 25–30 miles offshore of Port Aransas (TX), Port Fourchon (LA), and Dauphin Island (AL). Heart and spleen tissues were frozen in liquid nitrogen and returned to College Station where they were stored at 80 C. Otoliths were removed and individual fish aged by otolith-increment analysis (Wilson and Nieland 2001). Young red snapper of the year (age 0) were procured in the fall of 1999 and 2000 during demersal trawl surveys carried out by the National Marine Fisheries Service (NMFS). Tissue removal and storage was the same as for adult fish. Heart tissue from four Pacific red snapper, L. peru, used as outgroup in phylogenetic analysis, was kindly provided by A. Buentello (Centro de Investigaciones Biológicas del Noroeste Mar Bermejo, La Paz, Mexico). Total genomic DNA was extracted using a phenol/ chloroform method (Sambrook et al. 1989). A 590 base pair (bp) fragment of the mitochondrially encoded NADH dehydrogenase subunit 4 gene (ND-4) was amplified using standard polymerase chain reaction (PCR) protocols (Palumbi 1996a). Sequencing reactions were performed using the Big dye terminators (Applied Biosystems, Foster City, CA) and primers ND4LB (Bielawski and Gold 2002) and SnapHND4 (5’GTGGGCTTTAGGGAGTCAGAG-3’) for each DNA template. Cycle-sequenced products were electrophoresed on an automated sequencer (ABI 377, Applied Biosystems, Foster City, CA). Sequences were aligned and protein coding was verified using SEQUENCHER (v 4.1, Gene Codes, Ann Arbor, MI). The computer program MACCLADE 4.0 (Maddison and Maddison 2000) was used to identify individual mtDNA haplotypes. Sequences of all haplotypes were deposited in GENBANK. Accession numbers for the 60 haplotypes of L. campechanus are AY600304–AY600318, AY600320–AY600357, and AY600359–AY600365; accession numbers for 4 haplotypes of L. peru are AY600366–AY600369. Number of mtDNA haplotypes, haplotype frequencies, nucleon diversity (after Nei 1987), and nucleotide diversity were obtained using the software package ARLEQUIN (Schneider et al. 2000). Homogeneity of mtDNA haplotype distributions among cohorts within regions and among regions (cohorts pooled) was assessed via exact tests based on a Markov-chain procedure (1,000 dememorizations, 10,000 steps in Markov chain) and AMOVA, as implemented in ARLEQUIN. For the latter, significance of FST (among localities) and FSC (among cohorts within localities) was assessed by permutation (10,000 replicates). Neighbor-joining, maximum parsimony, and maximum-likelihood trees of red snapper mtDNA haplotypes were generated to help resolve relationships inferred from nested clade analysis and to determine which clades were interior/ancestral. Identification of interior/ ancestral clades is critical for determining geographic distance(s) between tip and interior clades in the highest nested level (the total cladogram nested together) and Fig. 1 Collection localities (black circles) of Gulf red snapper (Lutjanus c ampechanus) from waters offshore of Dauphin Island (Alabama), Port Fourchon (Louisiana), and Port Aransas (Texas) 594