Mar Biol (2012) 159:499–505 DOI 10.1007/s00227-011-1830-4
ORIGINAL PAPER
Phylogeography of the sub-Antarctic notothenioid Wsh Eleginops maclovinus: evidence of population expansion
Santiago Guillermo Ceballos · Enrique Pablo Lessa · Mariela Fernanda Victorio · Daniel Alfredo Fernández
Received: 8 June 2011 / Accepted: 20 October 2011 / Published online: 16 November 2011 © Springer-Verlag 2011
Abstract Phylogeography studies add insights into the geographic and evolutionary processes that underline the genetic divergence of populations. This work examines the geographic genetic structure of the Patagonian blennie, Ele- ginops maclovinus, a notothenioid (Perciformes) endemic to South American temperate and sub-Antarctic waters, using mitochondrial DNA cytochrome b sequences. We found 58 haplotypes in the analysis of 261 individual sequences of 833 base pairs in length. Among-population variance was very low (1.62%) and many haplotypes were shared between several populations across the species geographic range. Genetic diVerentiation was not consistent with a simple model of isolation by distance, possibly suggesting a lack of equilibrium between gene Xow and local genetic drift. The analysis of mismatch distributions, neutrality tests, and the Bayesian Skyline Plot showed a pattern consistent with a recent population expansion event that may have taken place during the Middle Pleistocene.
Introduction
Eleginops maclovinus (Cuvier and Valenciennes 1830),
known as róbalo in Argentina and Chile, is a notothenioid Wsh (Perciformes) of the monotypic family Eleginopidae. This marine Wsh is endemic to the coastal temperate and sub-Antarctic waters of South America with a range along the Atlantic and PaciWc Patagonian coasts from Valparaiso, Chile (33°S) (Pequeño 1989) to San Matias Gulf, Argentina (40°S) (Cousseau and Perrotta 2000). This eurithermic and euryhaline species that has been described as a protandrous hermaphrodite (Calvo et al. 1992; Brickle et al. 2005; Licandeo et al. 2006) inhabits costal waters, river mouths and estuaries (Gosztonyi 1980). On the Patagonian coast, E. maclovinus is a common Wsh species and an important component of many trophic webs, both as prey (Goodall and Galeazzi 1985) and as predator, feeding mainly on benthic invertebrates such as crustaceans and polychaetes, but also on algae and Wshes (Isla and San Román 1995; Licandeo et al. 2006; Martin and Bastida 2008; Pequeño et al. 2010). Additionally, E. maclovinus is important for the recreational and small food Wsheries throughout much of its distribution. Despite its ecological and socioeconomic importance, there is no information regarding its population dynamics and genetic structure, which must be understood for proper conservation and management.
Communicated by M. I. Taylor.
Electronic supplementary material The online version of this
article (doi:10.1007/s00227-011-1830-4) contains supplementary material, which is available to authorized users.
Many ecological and evolutionary features make
E. maclovinus an interesting species for a phylogeographic study. First, it is an ideal organism to study population responses to environmental variation associated with a broad latitudinal range. Second, E. maclovinus is considered the sister group of the Antarctic notothenioids Wshes (Near and Cheng 2008) that dominate the cold shelf waters of Antarctica (Eastman 2005) and provide a classic example of radiation in the absence of competition from most
S. G. Ceballos (&) · M. F. Victorio · D. A. Fernández Centro Austral de Investigaciones CientíWcas (CADIC), Bernardo A. Houssay 200, cp 9410, Ushuaia, Tierra del Fuego, Argentina e-mail: [email protected]
E. P. Lessa Sección Evolución, Facultad de Ciencias, Universidad de la República, 4225 Iguá, Montevideo, Uruguay
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other Wsh groups (Clarke and Johnston 1996; Eastman 2000). Therefore, this species likely presents several ancestral traits of the notothenioid radiation (Eastman and Lannoo 2008). And third, the continental shelf area where E. maclovinus is distributed nowadays was largely aVected by Quaternary glacial cycles. Events such as ice sheet calving into the ocean, retraction of the sea coast line and decrease in marine water temperature during glacial periods (Clapperton 1993; Rabassa 2008) might have aVected the habitat suitable for E. maclovinus and thus the population size and geographical structure. Demographic changes may leave genetics footprints in populations (Avise 2000) that can, therefore, be linked to climatic cycles. There are a growing number of studies that associate historical demography with climate changes in a variety of organisms from Patagonia such as grasses species (Jakob et al. 2009), rodents (Lessa et al. 2010), fresh water Wshes (Ruzzante et al. 2008; Zemlak et al. 2010) and crabs (Xu et al. 2009). A population genetic study of E. maclovinus would be an interesting contribution in order to generate an integrated scenario of how the biota has responded to historical climates changes in the entire Patagonian region.
To our knowledge, there are no phylogeographic studies on a single marine Wsh species along both Atlantic and PaciWc Patagonian coasts. In this work, we report the Wrst data on population genetics of E. maclovinus along its distributional range using mitochondrial DNA (mtDNA) sequences.
Fig. 1 E. maclovinus were collected at nine sites (triangles) along the
coast of Patagonia, South America. The approximated range distribution of the species is represented in the map by the shadow coastal area. Abbreviations: San Antonio Oeste (SAO)
Materials and methods
gene were ampliWed by polymerase chain reaction (PCR) from 261 individuals (21–36 per sampling site; Table 1). The PCRs used the forward primer MVZ 05 5Ј-CGA AGC TTG ATA TGA AAA ACC ATC GTT-3Ј (Smith and Patton 1991) and the reverse primer R1negra 5Ј-CCA GTA CTC CTC CAA GTT TGT CGG GG-3Ј, designed from the alignments of notothenioid cytb sequences. Thirty ꢀL of PCR reaction mixtures contained 15 ꢀL of total DNA (4 ꢀg/mL), 1 unit of Taq DNA polymerase (Promega), 1 £ Taq polymerase buVer, dNTPs (0.2 mM of each), forward and reverse primers (0.3 mM of each) and MgCl2 (2.5 mM). PCR used the following cycling conditions: an initial denaturation of 3 min at 94°C, 30 cycles of 30 s of denaturation at 94°C, 30 s of annealing at 50°C, and 1 min of extension at 72°C, and a Wnal extension of 5 min at 72°C. PCRs were performed in a 2720 Thermal Cycler (Applied Biosystems). PCR products were sequenced at Macrogen Korea with both PCR primers. Chromatograms were scored and analyzed using BioEdit (Hall 1999).
Sample collection E. maclovinus individuals (N = 261) were captured using trammel nets and gill nets at nine sites along the latitudinal range on the Atlantic and PaciWc Patagonian coasts: San Antonio Oeste (SAO) (40°50ЈS, 65°04ЈW), Puerto Madryn (42°46ЈS, 65°01ЈW), Rada Tilly (45°56ЈS, 67°32ЈW) Puerto San Julián (49°19ЈS, 67°42ЈW), Punta María (53°57ЈS, 67°26ЈW), Canal Beagle (54°49ЈS 68°10ЈW), Puerto Aysén (45°22ЈS, 72°51ЈW) Puerto Montt (41°32ЈS, 72°54ЈW) and Concepción (36°44ЈS, 73°11ЈW) (Fig. 1). Muscle samples were collected from each individual and preserved in 99% ethanol.
DNA extraction, PCR ampliWcation, and sequencing Total DNA extractions were performed with sodium dodecyl sulfate (SDS)-proteinase K-NaCl-alcohol precipitation (modiWed from Miller et al. 1988). Approximately 900 base pairs of the 3Ј end of the mitochondrial cytochrome b (cytb)
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Beast v1.6.0. The run consisted of 100 million generations sampled every 1,000 generations under the HKY + G model. Samples before the convergence zone were discarded.
Arlequin 3.11 was used to Wt the spatial expansion model (Schneider and ExcoYer 1999; ExcoYer 2004), to estimate the relative timing of expansion.
Table 1 Genetic variation at each site
Population
- n
- S
No. sin
- k
- H
ꢀ
- SAO
- 25
- 16
23 15 20 20 23 21 23 15 65
31
10 16 12
9
0.90 0.96 0.89 0.86 0.87 0.88 0.91 0.87 0.90 0.90
0.0047 0.0054 0.0026 0.0035 0.0036 0.0038 0.0042 0.0039 0.0032 0.0039
Pto. Madryn Rada Tilly Pto. San Julián Pta. María Canal Beagle Pto. Aysén Pto. Montt Concepción All pop.
27
- 25
- 10
15
7
24
- 38
- 11
16 16 14 13 58
- 36
- 14
10 17
9
Results
31 28
Variation among cytochrome b haplotypes
27
- 261
- 28
The Wnal data set consisted of 261 cytb sequences of 833 bp in length. An alignment of these sequences showed 65 variable sites, including 28 singletons and 37 parsimony-informative sites, which deWned 58 haplotypes (GenBank accession numbers JN010371, JN010428; Table 1; Online Resource 1). Eight of the 65 variables sites were non-synonymous changes that occurred in one (6), two (1) or three (1) individuals. Haplotype diversity was 0.90 for all individuals and ranged from 0.82 to 0.96 across sites. Nucleotide diversity was 0.0039 for all individuals and ranged from 0.0026 to 0.0054 across sites. The majority (28) of unique haplotypes (32) were deWned by single nucleotide changes.
n, sample sizes; S, number of polymorphic sites; No. sin number of singletons, k, number of haplotypes, H, haplotype diversity; and ꢀ, nucleotide diversity
Data analysis The number of haplotypes, the number of polymorphic sites and molecular diversity indices for cytb haplotypes, such as haplotype diversity (H) and nucleotide diversity (ꢀ), analysis of molecular variance (AMOVA), pairwise FST values, Mantel test, and Tajima’s D and Fu’s FS tests of neutrality were calculated in Arlequin 3.11 (ExcoYer et al. 2005). Observed and expected mismatch distributions under an exponential growth population model were obtained using DNAsp V5.1(Librado and Rozas 2009). A minimum spanning tree of the haplotypes was generated using the medianjoining method (Bandelt et al. 1999) in Network 4.6 (http://
Species-speciWc mutation rates (ꢁ) for Wve notothenioids species were obtained from calibrations of uncorrelated lognormal relaxed clocks using Beast v1.6.0 (Drummond and Rambaut 2007) under the HKY + I + G derived from JModeltest (Posada 2008) as the most appropriated model of sequence evolution with a data set of eight cyt b sequences: four representative E. maclovinus sequences, one each from the antifreeze glycoprotein (AFGP)-bearing
Antarctic notothenioids Dissostichus eleginoides, Notothe- nia coriiceps and Chionodraco rastropinosus, and one from
the early diverging notothenioid Cottoperca trigloides as the outgroup. For the calibration, the most recent common ancestor of the AFGP-bearing Antarctic notothenioids was set to 24 § 0.5 Mya (Janko et al. 2007; Near 2004) with a normal prior distribution. Parameter estimates were based on posterior probability distribution constructed by sampling the stationary distribution for 10 million generations every 1,000 steps.
Geographic genetic variation No Wxed diVerences were observed between populations, and many haplotypes were shared between several populations across the geographic sampled range (Fig. 2; Online Resource 1). Among-population variance was very low but signiWcant (1.62%; p = 0.019, AMOVA). Pairwise FST
Historical population sizes of E. maclovinus were estimated using the coalescent-based generalized Bayesian skyline plot (Drummond et al. 2005) as implemented in
Fig. 2 Minimum spanning tree connecting 58 mtDNA haplotypes. The area of each circle is proportional to frequency of the haplotype
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values ranged from 0.00 to 0.085, indicating low to moderate genetic diVerentiation between populations (Hartl and Clark 2007). A Mantel test did not show a signiWcant correlation between geographic distances and FST (r = 0.23, p = 0.096), thus failing to reveal a pattern of isolation by distance.
Phylogenetic relationships between haplotypes According to the minimum spanning tree (Fig. 2), haplotypes found in relatively high frequencies are present in many populations, reXecting the limited geographic structure. The Wve most frequent haplotypes are centrally located in the minimum spanning tree, and most of the remaining low-frequency haplotypes are separated from the common haplotypes by one or few mutational steps. This pattern, fairly star-like, probably reXects the imprinting of a past population expansion (Slatkin and Hudson 1991).
Fig. 3 Observed and expected mismatch distributions under a model of exponential growth for E. maclovinus from the Argentine and Chilean Patagonian coasts. Dashed lines correspond to the bound of a 90% conWdence interval (CI) for the expected mismatch distribution
past population expansion (Slatkin and Hudson 1991). The test of goodness of Wt did not Wnd signiWcant deviation from expectations under the spatial expansion model (sum of squared deviation = 0.001 and p = 0.83; Fig. 3).
Test of neutrality and mismatch distribution Overall values for both Tajima’s D and Fu’s FS were negative and signiWcant (D = ¡ 1.99, p < 0.01; FS = ¡ 25.93, p < 0.001). They were also negative in each population. Tajima’s D was signiWcant at Rada Tilly, Puerto San Julián, Beagle Channel and Puerto Montt, whereas Fu’s FS was signiWcant at Puerto Madryn, Rada Tilly, Beagle Channel, Puerto Aysén, Puerto Montt and Concepción (Table 2). Negative values of neutrality tests indicate an excess of low-frequency variants in relation to the mutation-drift equilibrium expectations and suggest a recent population expansion (Ramos-Onsins and Rozas 2002). The mismatch distribution of all sequences was unimodal, suggesting that demographic events in the past have forced coalescent events into a narrow time window in line with a history of a
Mutational rate estimation and historical population sizes It is possible to calculate the start of the population expansion if an estimate of the locus mutation rate per year (ꢁ) is available. We estimated ꢁ = 0.0054 substitutions per site per million years (95% highest probability density (HPD) 0024–0.0087). Using this ꢁ as a prior, Bayesian skyline plots (Fig. 4) estimated that population expansion started roughly 0.125 Mya (broadly, the results indicate that demographic expansion might have started from 0.1 to 0.175 Mya as could be inferred from the 95% HPD regions drawn in Fig. 4) and that the populations rapidly increased to the present size. The spatial expansion model suggested that the expansion was older, occurring 0.283 Mya (95%CI: 0.147–0.523 Mya).
Table 2 Values of Tajima’s D and Fu’s FS neutrality tests and corresponding p values
Population
- Tajima’s D
- Fu’s Fs
- D
- P
- Fs
- P
Discussion
- SAO
- ¡0.25
¡0.87 ¡1.61 ¡1.67 ¡1.24 ¡1.46 ¡1.15 ¡1.61 ¡1.10 ¡1.99
0.42 0.19 0.04 0.02 0.11 0.06 0.12 0.04 0.13 0.001
¡0.96 ¡5.79 ¡5.94 ¡1.35 ¡1.64 ¡6.46 ¡6.59 ¡5.29 ¡5.56
¡25.93
0.35 0.01 0.00 0.26 0.25 0.00 0.01 0.01 0.01 0.00
Populations with continuous distributions would show genetic structure if ongoing or historical processes have limited gene Xow or if they are under diversifying local selection (Avise 2009). Many marine species, which are expected to experience modest physical barriers to gene Xow and high dispersal potential, exhibit low levels of global population diVerentiation (Ward et al. 1994; Waples 1998). Although direct estimates are lacking, E. maclovinus likely has high dispersal capacity at adult, larval and egg stages. Adult vagility is expected to be high, since E. maclovinus adults
Pto. Madryn Rada Tilly Pto. San Julián Pta. María Canal Beagle Pto. Aysén Pto. Montt Concepción All populations
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systems (as those of species linked to coastal waters, such as E. maclovinus) have a reduced variance in geographical genetic attributes relative to 2-dimensional spatial systems, increasing the chance to detect a pattern of isolation by distance (Slatkin and Barton 1989). Nonetheless, we failed to detect a signiWcant correlation between FST and geographic distance. This result might come from a relatively recent event of demographic expansion coupled with fairly unrestricted gene Xow.
Although FST is an excellent measure of genetic diVerentiation among populations (but see Jost 2008 for qualiW- cations), inferences on the extent of migration based on FST are based on a number of assumptions (Whitlock and McCauley 1999) that are likely violated by the data in the present study. The estimate of gene Xow from FST is based on equilibrium expectations derived from neutrality theory as applied to idealized models of population structure (Slatkin and Barton 1989; Avise 2004). Our results (mainly the negative values of neutrality tests, the unimodal mismatch distribution, the absence of a pattern of isolation by distance and the event of rapid increase in population size indicated by the Bayesian Skyline Plot) are suggesting that E. maclovinus is far from both mutationdrift and migration-drift equilibrium and that may have only recently invaded the area it occupies. Therefore, the observed weak global population structure could reXect not only the actual level of gene Xow but also the historical connectivity of populations. As a result, FST-based estimates of gene Xow would be, almost certainly, higher than the actual gene Xow. As in any single locus analysis, we cannot rule out departures from strict neutrality as an alternative (or additional) cause of the observed patterns of genetic variation.
Population size changes at high latitudes are generally interpreted in relation to quaternary climatic cycles. Patagonia and Tierra del Fuego experienced signiWcant climatic Xuctuations during the Cenozoic, particularly since the Miocene. Pliocene and Pleistocene glaciations were frequent in this region. Glacial climatic episodes lasted long enough for the formation of a single, continuous mountain ice sheet that extended almost 2,500 km, at least between 36°S and 56°S. This ice sheet almost completely covered the Patagonian Andean ranges and extended over the piedmont areas to the east (and to the current submarine platform south of the Río Gallegos) and to sea level in the PaciWc side. The “Great Patagonian Glaciation” (GPG) that represents the maximum expansion of the ice in extra-Andean Patagonia developed sometime between 1.1 and 1 Mya (Rabassa 2008). Following the GPG, there is evidence of four major glacial episodes, post-GPG 1, post-GPG 2, post-GPG 3 and the “Last Glaciation” (LG) (following Coronato et al. 2004). Post-GPG 1 event would have taken place possibly before the Early–Middle Pleistocene boundary (>0.710 Mya). Post-GPG 2 attained
Fig. 4 Historical estimates of eVective population size (Ne) constructed using the Bayesian Skyline Plot based on mitochondrial cytochrome b haplotypes. The y-axis is the product of eVective population size (Ne) and generation length (ꢂ) in a log scale. The median estimate
(black line) and 95% HPD limits (gray lines) are shown
reach a maximum length of »80/90 cm (Gosztonyi 1974; Licandeo et al. 2006) and are highly mobile, at least in aquaria (personal observations). In addition, the E. maclovi- nus metabolic rate is comparable with that of other highly mobile sub-Antarctic teleosts (Vanella and Calvo 2005). As pointed out by Brickle et al. (2005), E. maclovinus is characterized by high fecundity and small pelagic eggs. Brickle et al. (2005) also suggested that, while inshore waters and estuaries are used for foraging, spawning may occur in deeper waters (30–100 m). In this case, the small pelagic eggs and early larval stages would be subjected to strong oVshore currents, which would enhance dispersal. Given the extended pelagic phases of many notothenioid Wshes, larval dispersal by marine currents has been suggested for a number of species in which populations genetic studies commonly found non-signiWcant diVerentiation across thousands of kilometers (Matschiner et al. 2009 and references therein).
E. maclovinus has been described as a protandrous hermaphrodite (Calvo et al. 1992; Brickle et al. 2005; Licandeo et al. 2006). In such sex-changing species, the naturally skewed sex ratio is expected to reduce eVective population size and increase genetic drift. As a result, Chopelet et al. (2009) hypothesized that sex-changing species would have more genetic structure than gonochoristic species. However, no diVerence in genetic structure was found among reproductive modes.
Our results are concordant with those of previous studies on other notothenioids or marine species which are expected to have high gene Xow between populations. The AMOVA revealed low global genetic variance among populations (1.62%), and allele sharing was extensive. In spite of the low global genetic structure, moderate but signiWcant genetic heterogeneity was observed in some pairwise FST values (data not shown). Nearly one-dimensional spatial