Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp
© Fraser et al; licensee BioMed Central Ltd. 2010
Received: 14 January 2010
Accepted: 1 July 2010
Published: 1 July 2010
South America's western coastline, extending in a near-straight line across some 35 latitudinal degrees, presents an elegant setting for assessing both contemporary and historic influences on cladogenesis in the marine environment. Southern bull-kelp (Durvillaea antarctica) has a broad distribution along much of the Chilean coast. This species represents an ideal model taxon for studies of coastal marine connectivity and of palaeoclimatic effects, as it grows only on exposed rocky coasts and is absent from beaches and ice-affected shores. We expected that, along the central Chilean coast, D. antarctica would show considerable phylogeographic structure as a consequence of the isolating effects of distance and habitat discontinuities. In contrast, we hypothesised that further south - throughout the region affected by the Patagonian Ice Sheet at the Last Glacial Maximum (LGM) - D. antarctica would show relatively little genetic structure, reflecting postglacial recolonisation.
Mitochondrial (COI) and chloroplast (rbcL) DNA analyses of D. antarctica from 24 Chilean localities (164 individuals) revealed two deeply divergent (4.5 - 6.1% for COI, 1.4% for rbcL) clades from the centre and south of the country, with contrasting levels and patterns of genetic structure. Among populations from central Chile (32° - 44°S), substantial phylogeographic structure was evident across small spatial scales, and a significant isolation-by-distance effect was observed. Genetic disjunctions in this region appear to correspond to the presence of long beaches. In contrast to the genetic structure found among central Chilean populations, samples from the southern Chilean Patagonian region (49° - 56°S) were genetically homogeneous and identical to a haplotype recently found throughout the subantarctic region.
Southern (Patagonian) Chile has been recolonised by D. antarctica relatively recently, probably since the LGM. The inferred trans-oceanic ancestry of these Patagonian populations supports the notion that D. antarctica is capable of long-distance dispersal via rafting. In contrast, further north in central Chile, the correspondence of genetic disjunctions in D. antarctica with long beaches indicates that habitat discontinuity drives genetic isolation among established kelp populations. We conclude that rafting facilitates colonisation of unoccupied shores, but has limited potential to enhance gene-flow among established populations. Broadly, this study demonstrates that some taxa may be considered to have either high or low dispersal potential across different temporal and geographic scales.
Oceanic ecosystems have historically been considered relatively open, with high connectivity among populations . Recent studies have, however, demonstrated considerable population structure in a variety of coastal taxa (see [2–5]; and references therein), indicating that connectivity among marine populations is often lower than previously assumed . Levels of connectivity in coastal ecosystems may be affected by a broad range of factors, including oceanography, geological history, habitat continuity, ecology and life history . The relative importance of these factors in structuring marine populations, however, remains largely unknown .
Genetic patterns of isolation-by-distance are common in the marine realm, with neighbouring populations generally more closely related to each other than to those further away, as the chance of successful dispersal decreases with increasing distance [3, 6]. Gene flow among populations with particularly stringent ecological requirements may also be impeded by habitat discontinuities [2, 8]. Extensive stretches of sandy beach might, for example, represent important biogeographic hurdles for rocky-shore marine taxa, even those with a planktonic larval stage [7, 9–12]. The genetic effects of habitat discontinuities should be greatest among populations of taxa with relatively low dispersal potential. Indeed, in several species of marine macroalgae with predicted low dispersal potential, discontinuities in suitable substratum have been linked to reduced gene flow among populations [13–15].
Although most macroalgae have only short-lived gametes or dispersive zygotes, some - particularly highly buoyant species - are hypothesised to be capable of long-distance dispersal via rafting of fertile adults (e.g., Fucus vesiculosus: ; Hormosira banksii: ; Macrocystis pyrifera: ). A broad-scale phylogeographic study of one such species, southern bull-kelp (Durvillaea antarctica), found evidence of recent (postglacial) recolonisation of much of the subantarctic, a feat almost certainly achieved by trans-oceanic rafting of adult specimens . Recolonisation of the subantarctic was inferred from extremely low levels of genetic structure among bull-kelp populations throughout this region, versus high levels of genetic structure in glacial refugia (e.g., New Zealand). Low levels of genetic structure of populations in historically glaciated regions, versus relatively high structure in unglaciated regions, is a signature of postglacial recolonisation that has been demonstrated in a wide range of marine and terrestrial taxa (reviewed by [20–24]). But if bull-kelp is able to disperse over long distances by rafting, how is high genetic structure maintained in refugial regions? Fraser et al.  suggested that the genetic structure observed in refugial areas may be largely a consequence of the density-blocking effects of established populations [20, 25]. In dense kelp populations, any limited available substratum is more likely to be colonised by zygotes from residents rather than those from rare, rafted individuals. Phylogeographic structure within refugial areas may therefore be driven more through isolation-by-distance, or breaks in habitat continuity, than by rafting dispersal. Rafting may, in contrast, enable long-distance dispersal and colonisation of unoccupied habitats.
Sample localities and number of samples sequenced from each for both mitochondrial (COI) and chloroplast (rbcL) DNA from D. antarctica.
#samples sequenced COI
#samples sequenced rbcL
32° 20' 43.92S
71° 27' 36.07W
32° 57' 27.31S
71° 33' 03.67W
33° 33' 3.06S
71° 37' 0.11W
33° 45' 57.27S
71° 46' 14.68W
34° 23' 37.79S
72° 01' 34.10W
34° 53' 12.37S
72° 10'' 07.14W
35° 19' 41.18S
72° 25' 59.41W
36° 29' 41.88S
72° 54' 36.26W
36° 36' 55.44S
73° 06' 29.74W
37° 35' 42.00S
73° 40' 9.00W
38° 20' 42.57S
73° 30' 30.27W
39° 23' 16.66S
73° 14' 26.60W
39° 49' 28.09S
73° 24' 18.68W
40° 35' 34.21S
73° 45' 01.30W
41° 56' 44.99S
74° 02' 22.02W
42° 40' 8.04S
74° 07' 18.55W
43° 33' 17.22S
74° 42' 55.69W
43° 54' 44.39S
74° 0' '7.31W
43° 59' '7.62S
73° 52' 23.30W
49° 09' 24.94S
75° 17' 48.99W
53° 39' 19.13S
72° 15' 29.02W
55° 59' 31.47S
67° 16' 14.98W
Network analyses of Chilean COI haplotypes recovered two parsimonious networks that could not be joined at ≥90% confidence limits, with one comprising only the Patagonian haplotype C-I. All other Chilean haplotypes (CII-CXIV) formed a single network (Fig. 3 shows these networks in the context of previously-published work ).
Two broad findings were revealed by our phylogeographic research of D. antarctica in Chile. First, substantial phylogeographic structure was observed in central Chile (hypothesis i). Genetic isolation among populations in this region appears driven by habitat discontinuities. Second, and in direct contrast to the pattern observed for central Chile, samples from Chilean Patagonia showed complete genetic homogeneity within and among localities (hypothesis ii). These Patagonian populations were deeply divergent to those from more northern (central Chilean) localities, and appear to have trans-oceanic ancestry.
Habitat discontinuity and population connectivity in central Chile
The substantial phylogeographic structure observed among central Chilean sampling localities of D. antarctica (Fig. 2) suggests a low level of genetic connectivity across this region (hypothesis i), a finding supported by the significant results of the isolation-by-distance test. Furthermore, the strong relationship between long beaches and genetic disjunctions in D. antarctica (Fig. 5) suggests that habitat discontinuity is likely a major factor controlling local genetic connectivity in this rocky-shore macroalga. Population connectivity of other kelp species may be similarly affected by interruptions in habitat: Faugeron et al. , for example, demonstrated genetic differentiation among populations of the kelp Lessonia nigrescens in northern Chile across a habitat discontinuity formed by a mine-waste disposal site. In the English Channel, Billot et al.  found evidence for reduced gene flow among populations of the kelp Laminaria digitata across habitat discontinuities. Patterns of genetic disjunction associated with habitat discontinuity have also been noted for numerous rock-dwelling taxa with predicted high dispersal abilities, including rocky-reef fish [7, 11], rock-pool copepods , and macroalgae (e.g., small-scale patterns of genetic structure in Phyllospora ), suggesting that for marine taxa, as observed for terrestrial plants [30, 31], dispersive life history alone does not necessarily lead to panmixia.
That habitat discontinuity appears to disrupt connectivity among central Chilean populations of D. antarctica is in direct contrast to the broad evidence of long-distance, trans-oceanic dispersal of this species in the subantarctic . Several biological factors may help to explain such a contrast in apparent dispersal ability/effectiveness. First, established and dense kelp populations may resist genetic input from rafted individuals  in a form of density-blocking [20, 25]. In such populations, limited substratum availability and high competition from local D. antarctica zygotes would suppress settlement of zygotes from such migrants. Conversely, shores swept clean by ice  or other large-scale disturbances would offer ample settlement opportunities for zygotes from rafted migrants. Although the genetic effects of density-blocking have yet to be demonstrated experimentally for brown algae, the complete genetic homogeneity of putative postglacially-recolonised populations (this study and ), and the absence of the Patagonian COI haplotype (CI) from central Chilean populations, indicate that such a process is likely to be occurring. Second, although D. antarctica is clearly an effective long-distance disperser, there may be differences in reproductive viability of rafts across latitudinal gradients. Numerous reports suggest that D. antarctica has an extended period of fertility in the subantarctic versus mainland New Zealand or Chile (see references in ), perhaps facilitated by longer optimal reproductive conditions in colder waters. Observations by Macaya et al.  suggest that detached rafts of another kelp, Macrocystis pyrifera, lose reproductive activity at high temperatures, a finding supported by Rothäusler et al. . If D. antarctica rafts are similarly affected by high water temperatures, fewer zygotes from immigrant individuals may be available to colonise central Chile than in the relatively cold waters of Chilean Patagonia (Fig. 1).
Local genetic structure within and among central Chilean D. antarctica populations could additionally be influenced by a range of processes such as seasonal variation and patchy recruitment  or harvesting [34–36]. While the results from Bustamante & Castilla  and Castilla et al.  underline the importance of short-distance dispersal in local population dynamics, coastal islands might serve as stepping stones allowing dispersal across long stretches of sandy beaches. Indeed, the only locality pair separated by a long beach that did not show a genetic disjunction (Lebu-Tirua) is in the immediate vicinity of a large coastal island (Isla Mocha) that may effectively connect the two populations despite the beach barrier. Interestingly, Constitución, flanked by long beaches on both sides, was genetically distinct from adjacent localities but not from some more distant localities (Cartagena, Montemar and Pichicuy). These populations, on the northernmost edge of the range of D. antarctica in Chile, may be sensitive to any changes in water temperature. Changes to the northern range limit of an Australian congeneric, D. potatorum, have been linked to warming waters in recent years . The northern populations of D. antarctica in Chile (Cartagena, Montemar and Pichicuy) may thus be somewhat ephemeral in the long term, and could have been relatively recently colonised by kelp drifting from southern populations (e.g., Constitución) in the north-flowing Humboldt Current.
Major genetic disjunction in southern Chile
Our phylogeographic analyses of Chilean D. antarctica populations indicate a biogeographic break in northern Chilean Patagonia (44° - 49°S), with both mitochondrial and chloroplast DNA phylogenies revealing a deep genetic disjunction between samples from southern Patagonia and those from central Chile (Fig. 2). Although the precise geographic location of this major genetic disjunction cannot be pinpointed with this present dataset, a biogeographic break in the vicinity of the Golfo de Penas/Taitao Peninsula (46.5°S; Fig. 2) has previously been noted [38, 39]. More recently, Lancellotti and Vásquez  suggested this feature may represent the southern boundary of the transitional zone, separating it from the cold-temperate southern waters south of 46°S. The hypothesis of a biogeographic break at Taitao Peninsula has been supported by several recent shallow-marine surveys of Cnidaria in southern Chile [41, 42], with samples showing distinct changes in species composition to the north and south of about 46°S. In a recent study of the density of drifting kelp in channels north of Taitao Peninsula, Hinojosa et al.  suggest that D. antarctica rafts are driven by both surface currents (primarily westward) and wind (primarily eastward) through the fiords. Taitao Peninsula, however, projects across the dense system of channels that could otherwise potentially allow mixing and north-south transport of drifting D. antarctica within the fiords.
The deep genetic disjunction between D. antarctica samples from southern Patagonia and those from central Chile raises the question of the taxonomic status of these two divergent lineages. A recent study of D. antarctica revealed that this taxon comprises two ecologically, morphologically and genetically distinct forms in New Zealand . Given that the genetic disjunction between Patagonian and central Chilean D. antarctica (4.5 - 6.1% for COI) exceeds the divergence observed between the co-occurring, genetically-distinct forms in New Zealand (3.0 - 3.8% for COI: ), it is possible that the distinct Chilean lineages represent reproductively-isolated species, and future studies should assess any physiological, ecological or life history differences between them. Regardless, the phylogeographic contrasts between these lineages are intriguing, with negligible genetic structure observed throughout sampled Patagonian populations (a single haplotype for COI at all five localities across some 1000 km of shoreline), versus high structure further north (eleven COI haplotypes across approximately 1400 km).
Postglacial recolonisation of coastal Chilean Patagonia
The complete genetic homogeneity observed in D. antarctica from all localities south of latitude 44°S (the region covered by the Patagonian Ice Sheet at the LGM: Fig. 1), compared with substantial phylogeographic structure among populations in central Chile for COI (Fig. 2), strongly supports a hypothesis of postglacial recolonisation of Chilean Patagonia (hypothesis ii). Such events are typically marked by low levels of genetic structure in recolonised versus refugial areas (reviewed by [20–24]) although, to date, few studies have been carried out in the Southern Hemisphere . Recolonisation of Patagonia appears to have occurred from a trans-oceanic source, rather than from geographically proximate areas in central Chile. The Patagonian COI haplotype C-I also occurs on numerous subantarctic islands (Fig. 3, and see ), and is more closely related to haplotypes found in the New Zealand subantarctic region than to other Chilean haplotypes , suggesting the New Zealand region as a source, with transport facilitated by the Antarctic Circumpolar Current (Fig. 1) [46–49].
Although genetic evidence of postglacial recolonisation has previously been identified from a variety of Patagonian terrestrial and freshwater taxa, including fish (galaxiids: [50–52]; percichthyids: [53, 54]), lizards , and plants [56–58], this is the first study to reveal evidence of postglacial recolonisation of a Chilean Patagonian marine taxon (but see recent findings on the likely impacts of glacial cycles on marine dispersal by diadromous fish in Patagonia ). Additionally, in comparison with Fraser et al. , who inferred recolonisation of several subantarctic islands by Durvillaea after extirpation by sea ice, this work shows that the glacial (i.e., land-based) ice during the most recent ice age may also have driven kelp population extinctions. If populations of D. antarctica in southern Chile were indeed destroyed by the Patagonian Ice Sheet during the last glacial period, numerous other coastal taxa may have been similarly affected. Intriguingly, a broad-scale phylogeographic study of the rocky-shore gastropod Concholepas concholepas , found no evidence of recent (post-LGM) recolonisation of Chilean Patagonia. Perhaps the habitat of this molluscan species, extending to 40 m below sea level , enabled it to survive throughout the last ice age in regions where more intertidally-restricted taxa were eliminated by ice. Future studies should aim to assess whether a pattern of postglacial recolonisation is common among other subtidal and intertidal species in southern Chile.
Our understanding of evolutionary processes relies largely on our knowledge of the factors that drive and maintain genetic variation and population connectivity. Marine systems can present paradoxical patterns of genetic connectivity, with taxa that apparently have low intrinsic dispersal capacities occasionally showing broader geographic ranges than highly dispersive taxa [61–63]. In such cases, passive dispersal by rafting may explain the broad distributions of otherwise non-dispersive species . The results of the current study suggest that some taxa cannot necessarily be classified as either 'high' or 'low' dispersal organisms, and that mechanisms of dispersal may vary across temporal and geographic scales. Bull-kelp (D. antarctica) is capable of long-distance dispersal via rafting of fertile adults, as evidenced by the trans-oceanic ancestry of populations throughout postglacially-recolonised Chilean Patagonia (and subantarctic islands ). Intriguingly, this dispersal capacity facilitates colonisation of as-yet unoccupied rocky shores, but does not enhance connectivity among established populations. Long-established populations, such as those along the coast of central Chile, seem strongly influenced by the isolating effects of geographic distance and habitat discontinuities, indicating relatively poor inter-population connectivity.
Sample collection, DNA extraction and sequencing
164 samples of D. antarctica were collected from 24 localities along the coast of Chile, from Pichicuy (32°27'37"S) to Cape Horn (55°59'31"S) (Fig. 2, Table 1). These localities encompassed most of the Chilean range of this species, which extends from Los Vilos (31°54'27"S; 60 km north of Pichicuy) to Cape Horn. The data from seven of the localities in Chile (Cucao, Bahia Mansa, Punta Loncoyen, Tumbes, Constitución, Montemar and Pichicuy) were included in previously published analyses  but are here reanalyzed in-depth in the light of extensive additional sampling (106 new samples from 17 new localities). Samples consisted of small (< 2 cm2) pieces of tissue cut from the tip of healthy fronds of attached D. antarctica, and were preserved by desiccation in either 96% ethanol or silica gel beads. DNA extraction, amplification, purification and sequencing were performed as described in Fraser et al. . A 629 bp region of mitochondrial cytochrome c oxidase I (COI) was amplified using primers GazF1 and GazR1  for all samples. In addition, an 886 bp region of chloroplast rbcL was amplified using primers KL2 and KL8  for samples from three localities in Chilean Patagonia, and analysed with previously-published sequences from central Chile (Pichicuy, Montemar, Constitución, Tumbes, Punta Loncoyen and Cucao) (Table 1).
Phylogenies for each DNA dataset were constructed using maximum-likelihood (ML) and Bayesian analyses, and included outgroup sequences from Durvillaea willana (South Island, New Zealand; GenBank accessions: EU918569 for COI and EU918578 for rbcL), Durvillaea potatorum (Tathra, southeastern Australia; GenBank accessions: FJ873092 for COI and FJ872990 for rbcL) and Fucus (GenBank accessions: F. vesiculosus AY494079 for COI and F. gardneri AF195515 for rbcL). To place the new Chilean sequence data in a wider context, published D. antarctica DNA sequences (GenBank accessions FJ550086 - FJ550112) from seven of the localities in central Chile, and numerous localities around the subantarctic and New Zealand, were included in the analyses (Fig. 2). Note that the unique COI and rbcL haplotypes reported from the Crozet Islands by Fraser et al.  were later found to be erroneous, and were in fact identical to the widespread haplotypes C-I and R-I; this error was corrected for the present analyses. ML analyses were performed using PhyML  with a TrN + I  model for both COI and rbcL (proportion of invariable sites estimated, Nst = 6) as selected by the AIC of Modeltest 3.06 . Node support was estimated by bootstrapping , with heuristic analysis of 1000 replicate data sets (Fig. 2). Bayesian posterior probability (PP) values were calculated using MRBAYES 3.1.2  and are shown on the ML phylogenies (Fig. 2). Markov chain Monte Carlo (McMC) searches were performed, with four chains of 5,000,000 generations and trees sampled every 100. The first 10,000 trees sampled were discarded as 'burn-in,' as determined using Tracer v1.4 , while a consensus topology and posterior probability values were calculated with the remaining trees. Unrooted statistical parsimony networks were built using TCS 1.21 . All unique DNA sequences obtained during this study were deposited with GenBank (accession numbers for all Chilean D. antarctica COI and rbcL sequences used in this study: FJ550093-FJ550095; FJ550097; FJ550099; FJ550119; HM103936-HM104173).
Analysis of isolation-by-distance was performed on data from the 19 localities in central Chile (north of 44°S) via the Mantel  test, implemented in GenAlEx6 , using raw (D) average pairwise differences  (calculated using Arlequin version 3.0 ) versus coastal distance (not including deep bays with narrow, < approximately 2 km, openings) among sample localities. Linearised population pairwise FST values could not be used in the Mantel test: several localities were genetically monomorphic for different haplotypes, and pairwise comparisons between such fixed populations gave an FST of 1.0; hence for these locality pairs no linearised FST values (FST/(1 - FST), ) could be calculated.
Approximate measurements of the lengths of all beaches (coastal stretches of uninterrupted sand, gravel or pebbles) between pairs of adjacent rocky coastal localities in central Chile were made using the 'path ruler' tool in Google Earth http://earth.google.com/ to assess the continuity of suitable rocky shore habitat for D. antarctica among localities. As Chilean shores south of about 43°S are almost completely rocky, with few sandy beaches and, moreover, many wide oceanic channels between islands and peninsulas, measurements of beaches were only made for continental Chile and the coast of the Great Island of Chiloé (north of 43°S). The following analysis was performed only on data from sampled localities in this region (Pichichuy, at 32° 20', to Cucao, at 42°40' S). The isolating effects of beach length and total coastal distance between localities in central Chile were assessed by logistic regression. Adjacent locality pairs were first classified binomially as either genetically disjunct (D ≥1.0) or not (D < 1.0). Under this definition, locality pairs not sharing any haplotypes were considered genetically disjunct, whereas those with shared haplotypes were not considered disjunct. Logistic regression was then carried out using R , using the logistf add-on package, with the model: 'genetically disjunct' ~ 'maximum beach length between adjacent localities' + 'coastal distance between adjacent localities'. This analysis enabled assessment of the relative abilities of total coastal distance, versus beach length, to predict whether or not adjacent localities were genetically disjunct.
We are extremely grateful to all who assisted with this research. For field support/sample collection, we thank: Emma Newcombe and Carlos Olavarría (Centro de Estudios del Cuaternario, Punta Arenas, Chile) for advice and collections from Cape Horn and southern Patagonia (Cruceros Australis and Whalesound provided suport for these collections); David Yáñez Jaramillo (Marine Botany Laboratory, Universidad Católica del Norte, Coquimbo, Chile) for assistance with fieldwork; Iván Hinojosa (Universidad Católica del Norte, Coquimbo, Chile), Patricio Díaz and Hector Pavez (Universidad Austral de Chile, Valdivia, Chile) for collections from Patagonia; Erasmo Macaya Horta (Victoria University of Wellington, New Zealand) for facilitating many collections; Thanks to Tania King for laboratory assistance, to Raisa Nikula for advice, and to Shinichi Nakagawa and Catherine Grueber for help with statistical analyses. Comments from Graham Wallis and two anonymous reviewers also helped improve the MS. This work was funded by Marsden contract 07-UOO-099, Department of Zoology and University of Otago Research grants to JMW; a Department of Zoology funding allocation to CIF; and Allan Wilson Centre for Molecular Ecology and Evolution funds to HGS.
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