Comparison of genetic barriers for black and yellowtail rockfishes
Our population genetic study of black rockfish found evidence of more than one stock. In fact, based on microsatellites, there may be at least three populations along the species range; one concentrated in the south (U.S. West Coast), one that is concentrated at a single collection (Brookings, OR), and one that is concentrated in the north (Western Alaska). Our analyses of both mitochondrial sequences and nuclear microsatellite genotypic data from black rockfish collections reveal the presence of abrupt genetic clines (i.e., short isolation-by-distance trends) centered on three different geographic locations. Two genetic clines occur on relatively small geographic scales within the U.S. West Coast of our study (within 2–3 degrees latitude) and all three are significant isolation-by-distance correlations using a minimum of four neighboring collections. A relatively steep genetic cline based on high FST/(1- FST) revealed by our mtDNA dataset was centered between latitudes 38 to 42 (collections 3 to 7). This is similar to the pattern in yellowtail rockfish which exhibited a trend from between those same latitudes that appeared centered at Cape Mendocino (Latitude 40.5; Hess et al. 2011). However, unlike yellowtail rockfish, this genetic cline was not as steep [0.8 versus 1.8 FST/(1- FST) per 1000 km], it did not divide the region into two separate regional stocks, and it may be centered slightly further south (between collections 4 and 5, Point Arena). Further, the composition of mitochondrial haplotypes that comprise this cline resemble a staircase that begins in the southernmost range (San Francisco, CA) as relatively high frequency of southern haplotypes, which then decrease rapidly going northward (Crescent City, CA), and then again increase rapidly to a high frequency of southern haplotypes (Charleston, OR). These two transitions represent the two clines exhibited in the mitochondrial structure. The microsatellite genetic structure also shows a cline equal to the value [0.5 FST/(1- FST) per 1000 km] and the location (between collections 5 and 6 near Cape Mendocino) of that displayed in yellowtail rockfish structure. However, this black rockfish microsatellite cline is similar to the mitochondrial clines in the way it resembles an upward/downward staircase and does not split the U.S. West Coast range into two stocks unlike the cline in yellowtail rockfish.
Finally, a second significant microsatellite genetic cline was centered on the region between the Alaskan and continental U.S. collections. This cline appeared to be less steep than the US West Coast genetic cline but it is unclear whether this is simply due to a lack of samples between Neah Bay, WA and Yakutat, Alaska. The entire Canadian range is unsampled and may reveal more abrupt transitions if data were available.
Northward range expansion
The microsatellite data from the yellowtail rockfish study (Hess et al. 2011) had provided some indication that northern range expansion may have been part of the historical processes affecting population structure in the species. We would generally expect low genetic diversity in the northern collections of a species that has experienced rapid range expansion. This analysis provides evidence of a recent expansion of black rockfish into Alaska. First, the cytochrome gene diversity in this study was consistently lower in Alaskan collections vs continental U.S. collections. In fact, mtDNA gene-diversity appears significantly lower in the northern portion of the species range starting north of the Columbia River at the border of Oregon and Washington and continuing into Alaska. Second, in a previous microsatellite study by Seeb and Seeb (2005) they find a decreasing allelic richness going west into Alaska. In contrast, we did not find a decreasing trend over all loci with regards to allelic richness in our microsatellite data (we used a different set of loci than Seeb). At most there was a single locus 15 − 8 that showed a decreasing trend of gene diversity in Alaska, but a different locus showed a significant opposite trend. We would expect low gene diversity in more recently expanded areas compared to areas that have maintained relatively stable effective population size over a longer time. These results may indicate longer population stability in the south as compared to the north.
The NCPA could not resolve whether isolation by distance or range expansion/colonization explains mtDNA variation due to insufficient genetic variation. The haplotype H was shown to be distributed relatively far from its parent haplotype (A) at the extreme end of the range in Western Alaska, which is a pattern typical of range expansion. However, robust testing requires more than just a single haplotype to show this pattern before it can be confidently interpreted. The NCPA did show a role for the process of restricted gene flow by isolation by distance. At the oldest temporal level (i.e. total cladogram level), isolation by distance gene flow explains the distribution of genetic variation.
Glaciation cycles have been hypothesized to affect genetic structure and speciation in other rockfish species. First, Rocha-Olivares et al. (1999) discussed how the presence of rosethorn rockfish (S. helvomaculatus) in Alaska may be the result of a northward expansion from a subgeneric center of the radiation south of 38 N. Second, copper rockfish population structure showed evidence of range expansion into Puget Sound after marine conditions were reestablished (Buonaccorsi et al. 2002). Third, speciation of thornyhead rockfishes (genus Sebastolobus, closely related to Sebastes) may have resulted from glacial cycles inducing vicariant events (Stepien et al. 2000).
Similar to our microsatellite results, an abrupt genetic cline was described in black rockfish within Alaska. Seeb and Seeb (2005) found support for a genetic discontinuity at the Alaska Gyre and suggested the direction of ocean currents in the Gulf of Alaska (GOA) restricts dispersal. The main results were: 1) significant pairwise FST values between all western GOA collections and every southeastern Alaska and Pacific Northwest collection, and 2) a trend toward decreasing allelic richness starting from the Pacific Northwest to the western GOA collections. However, ocean currents acting as gene flow barriers would not fully explain the second result. An alternative explanation is the western GOA collections were founded by a relatively small group of individuals (lacking in genetic variation), thus resulting in the observed decrease in allelic richness. One reason for expecting this founder scenario in the Alaskan range of this species is due to the last glacial maximum (LGM) that occurred just 20,000 years ago, which may have made this northern coastal habitat unsuitable to nearshore species. Glaciers and their associated ice shelves are hypothesized to have covered much of the continental shelf between the Alaska Peninsula and British Columbia (Mann and Hamilton 1995).
Extinction and recolonization events
So far, we have emphasized short isolation-by-distance trends along the U.S. West Coast in the genetic structure of black rockfish. However, a couple collections are genetically divergent from neighboring collections in mtDNA (collection 9) and microsatellite (collection 8) datasets. These collections had relatively large sample numbers (n ≥ 50); yielded consistently high FST levels across a majority of collections in the dataset, including their nearest neighboring collections; and were both located in southern Oregon on either side of Cape Blanco.
The collections 8 and 9 do not appear to be part of any regional isolation-by-distance trends but appear to be isolated events at small spatial scales. These single divergent collections that lacked isolation-by-distance trends with surrounding collections are unlikely to be explained by sampling error, rather they were likely the result of local extinction and recolonization events. As few collections that had low effective population size, including collection 8 at Brookings, OR, provides evidence of local extinction and recolonization events. Additionally, collection 8 shows a deficit in heterozygosity across several loci that may be indicative of a recent increase in population growth from low effective population size. Collection 8 was genetically differentiated from all other collections in the species range according to the microsatellite data. Interestingly, a previous study of black rockfish identified Brookings, OR as a location with aberrant collections (Miller et al. 2005). Miller et al. (2005) found HWE deviations at microsatellite loci Spi4 and Spi10. In our study, collection 8 at this location of Brookings was differentiated from surrounding collections, however, none of the p-values were significant in tests for deviation of HWE. Results from BOTTLENECK simulations showed only collection 8 had significant heterozygosity deficit at more than four loci. We suggest that this area near Brookings, OR may have undergone a recent increase in population size from a small group of founders that could account for collection 8 being highly genetically differentiated from all other collections in this study and the fact that there are deficits of heterozygosity across multiple loci.
Despite these extinction and recolonization events, the overall population structure of black rockfish compared to yellowtail rockfish was not substantially higher as measured by overall FST. For example, based on microsatellites black rockfish had an overall FST of 0.017 (95% C.I: 0.011–0.022) compared to yellowtail 0.011 (95% C.I: 0.008–0.015). Based on mitochondrial DNA black rockfish data showed that splitting the dataset between collections 4 and 5 and making collection 9 into a third region yielded an FCT (0.169, p < < 0.001) that was lower than the FCT represented by splitting the yellowtail rockfish range at Cape Mendocino (FCT = 0.32, p < < 0.001; Hess et al. 2011). Whether the depth preference differences between these species led to an overall greater number of extinction and recolonization events in black rockfish is an interesting question worth further consideration. However, regardless of possible higher frequency of these extinction and recolonization events, these events did not lead to greater overall genetic differentiation across the range but rather greater localized differentiation of neighboring sites. For example, the concentration of southern haplotypes at the southern end of the range appears suddenly absent near Point Arena (between collection 4 and 5) then continues to be absent until further north around collection 8 and 9 at Cape Blanco, before disappearing again at northern neighboring collection at Newport, OR (10). Stochasticity from recurrent extinction and recolonization events would tend to create a disrupted pattern of haplotypic composition along the coast.
One possible cause of extinction and recolonization may be related to levels of anoxia observed in the Oregon range of black rockfish (Chan et al. 2008). Dissolved oxygen measured from 0–800 meters depth during upwelling season (mid-April to mid-October) between 42–46° N latitude (approximately the area between collection 7 and 11, Fig. 1) crossed the severe hypoxia threshold (below 0.5 ml L− 1) in 2006, which was a rare event from 1950–1999 but has increased from 2000–2005 (Chan et al. 2008). Chan et al. (2008) reported that this severe hypoxic event affected all their cross-shelf transect lines between 44.25°N and 45.00°N (approximately the area between collection 9 and 11, Fig. 1), extending from the shelf break to the inner shelf (under 100 m depth) and encompassing at least 3000 km2. Further, Chan et al. (2008) showed there was a complete absence of all fish from the rocky reefs normally occupied by rockfishes when they conducted submersible surveys in August 2006. This particular event would have been most likely to affect collection 10 that was obtained in the summer of 2005 within the hypoxic region and before that area was found in summer 2006 to be vacant of rockfishes (Chan et al. 2008). Black rockfish would have been one of the species impacted by this phenomenon as adults mostly occur in less than 55 m depth (Love et al. 2002). Interestingly, collection 10 had significant pairwise FST based on mtDNA, and lower mtDNA gene diversity compared to its two neighboring collections 9 and 11. Fish may not suffer direct lethal effects from these hypoxic conditions since they can move to avoid them, but the effects can be similar to extinction and recolonization events. When a large area of habitat becomes unsuitable, periods of displacement can be followed by replacement, but not necessarily by a representative sample of the displaced individuals.
It is possible that aspects of the reproductive biology of black rockfish, particularly bet-hedging strategies (e.g., Sogard et al. 2008) combined with sweepstakes type recruitment mechanisms (e.g., Markel et al. 2006), have influenced the genetic disruptions we have observed. The period of parturition (when larvae are extruded) occurs between mid-January and mid-March with a peak in February and older females tend to release larvae earlier than younger females (Bobko and Berkeley 2004). It also appears that faster growth and higher survival was linked to older females likely due to contributing a larger energy storage oil globule to larvae (Berkeley et al. 2004). In this way, localized areas may receive segments of larval recruitment originating from a relatively small numbers of adults.
The influence of seascape on genetic structure
The three locations of steep genetic clines from this study (two in Central California close to Point Arena and Cape Mendocino and one in the region between Alaska and Continental U.S.) have all been discussed previously as locations of putative mesoscale oceanographic dispersal barriers in population genetic studies of rockfish (reviewed by Gunderson and Vetter 2006, Hyde and Vetter 2009). The complete list of barriers includes Alaska Gyre, Queen Charlotte Sound, Puget Sound, the Cape Mendocino jet (e.g., yellowtail rockfish, Hess et al. 2011), and the Southern California Eddy (e.g. cowcod rockfish, Hess et al. 2014; sunset rockfish, Longo et al. 2022) and these locations have all been shown to correlate to genetic discontinuities in rockfishes (Gunderson and Vetter 2006). Even outside of the rockfish genus, other marine taxa (fishes and invertebrates) also show genetic discontinuities at these locations (Hare and Avise 1996; Arndt and Smith 1998; Lecomte et al. 2004; Marko 2004; Cimmaruta et al. 2005; Hickerson and Cunningham 2005; Hickerson et al. 2006; Wilson 2006; Petersen 2007). Besides correlative evidence from genetic studies, Point Conception and Cape Mendocino (Briggs 1974, Williams and Ralston 2002, Cope 2004) are observed to be biogeographic breaks where species ranges terminate. In addition, Cape Mendocino and Cape Blanco are regions where groundfish species assemblage structure has been found to shift (Tolimieri and Levin 2006).
The possible mechanisms responsible for the way in which these locations could act to limit dispersal may be due to currents (Magnell et al. 1990; Marchesiello et al. 2003, Longhurst 2007) or bathymetric features such as submarine ridges and canyons (Williams and Ralston 2002). Longhurst (2007) defined a series of geographic compartments within the California Current Ecological Province and these coast upwelling regions explained genetic patterns in the vermillion rockfish species complex (Hyde and Vetter 2009). At various capes along the west coast and particularly at Cape Mendocino, there are major upwelling quasi-permanent eddies (Marchesiello et al. 2003) and they are strongest in spring and summer when rockfish juvenile recruitment occurs. For regions around Monterey and Cape Mendocino California there is also a decrease in total habitat in waters shallower than 200 m, which affects the common depths inhabited by both yellowtail and black rockfish (Williams and Ralston 2002).
The collections that were genetically divergent from neighboring collections (collection 8 at Brookings, OR and collection 9 at Charleston, OR) do not appear to be a result of a major dispersal barrier that disrupts connectivity in a way that splits this species into two separate stocks. However, Cape Blanco is located in between Brookings and Charleston, OR and there may be a localized isolating effect of currents in the vicinity of Cape Blanco that are sufficient in cutting off recruitment from neighboring areas to produce a recruitment sink. In addition, a large swath of sandy habitat between Charleston and Newport separates rocky habitat that is more suitable for black rockfish. Copper rockfish also show a genetic discontinuity between Charleston and Newport, Oregon (Buonaccorsi et al. 2002; Johansson et al. 2008). Aside from rockfish, four species of Pacific salmonids, Oncorhynchus mykiss (steelhead trout), O. clarki (cutthroat trout), O. kisutch (coho salmon), and O. tshawytscha (Chinook salmon) share similar Evolutionarily Significant Unit (ESU) designations and the northern border of ESU III is demarcated at Cape Blanco, OR.
Past genetic studies on black rockfish
There have been several genetic studies conducted across portions of the range of black rockfish. Four of these studies found significant genetic structure based on FST values calculated overall collections: FST = 0.011 (P < 0.001), ten microsatellites, eleven collections from Oregon to Aleutian islands (Seeb and Seeb 2005); FST = 0.018 ± 0.004 (p < 0.001), seven microsatellite loci, four collections from Oregon and Washington (Miller et al. 2005); and FST = 0.013 (P < 0.05), fourteen allozyme loci, eight collections from northern Oregon (Don Bodenmiller, ODFW pers. comm.); and FST = 0.002 (p < 0.001), eight microsatellite loci, eight collections from Oregon to Vancouver Island, B.C. (Lotterhos et al. 2014). Additionally, a stock identification study conducted in 1995–1997 by WDFW genotyped ten collections from northern California to southern British Columbia for twenty allozyme loci (Farron Wallace, WDFW pers. comm.). Multidimensional scaling (MDS) analysis of genetic distances (Nei, 1978) revealed three major geographical groupings: 1) north of Cape Falcon, 2) south of Cape Falcon off the Oregon coast, and 3) a single collection from northern California (Farron Wallace, WDFW pers. comm.).
These studies provide evidence that black rockfish exhibits some degree of structure throughout the range and some of the stock divisions that have been identified are shared across studies. The main conclusions of Miller et al. (2005) were that the collection from southern W.A. was genetically divergent from all other collections from southern Oregon. Seeb and Seeb (2005) concluded that a discontinuity occurred between Southeastern A.K. and Western G.O.A collections. Farron Wallace (pers. comm.) found a genetic boundary at Cape Falcon (just south of collection 11). No significant pairwise FST values were found in the smaller geographic scale study confined to northern Oregon including collections located on either side of Cape Falcon (Don Bodenmiller, pers. comm.). Finally, Lotterhos et al. (2014) found that the collection at the extreme southern end of their study region, near Cape Blanco, was divergent from the rest of the range.
Implications for fisheries management of black rockfish
Stock assessments are critical for management of marine fishes including black rockfish, as their purpose is to collect and analyze demographic data to characterize changes in abundance of fishery stocks. In the most recent stock assessment of black rockfish (Cope et al. 2016), Black rockfish was divided into three stocks stratified by the borders of California and Oregon and the borders of Oregon and Washington along the continental U.S. coast. The northern portion of the range is assessed and managed by Alaska Department of Fish and Game (ADFG) and by Department of Fisheries and Oceans for the portions of the range in Alaska and Canada, respectively. ADFG assesses the species as three separate stocks in the Western Region: Kodiak, Chignik, and the South Alaskan Peninsula Area-Eastern District (Mattes and Sagalkin 2007).
The continental U.S. black rockfish assessments have in the past used a tagging study and allozyme genetic study (Wallace et al. 2007) as a basis for assessing black rockfish as two different stocks separated by Cape Falcon, OR (between collections 10 and 11). The more recent assessment considers three stocks and uses the state borders (CA and OR border is between collections 7 and 8; OR and WA border is between collection 11 and 12), however, our genetic results provide basis to break California into two stocks at Point Arena (between collections 4 and 5). In addition, our genetic results within Oregon provide support for another stock boundary near Cape Blanco (between collections 8 and 9). Alaska is already managed separately from the continental U.S., and until more work can be performed, results from Seeb and Seeb (2005) showing a stock boundary west of Yakutat seem reasonable. A greater level of stratification along these suggested boundaries would create five black rockfish stocks along the U.S. continental coastline which may complicate stock assessments. However, the potential for gene-flow barriers identified as genetic breaks in this study may indicate that abundance trends of rockfish populations on either sides of these genetic breaks may be behaving in independent ways and could benefit by being assessed separately.
Concluding remarks
Our population genetic study on black rockfish establishes this species as an example of a marine species having more genetic structure on both fine and coarse spatial scales than would be expected given the large dispersal potential of their pelagic larval and juvenile life stages. We demonstrated how evolutionary processes such as restricted gene-flow with isolation by distance, range expansion, and extinction and recolonization appear to have influenced the observed genetic patterns. While black rockfish and yellowtail rockfish have overlapping ranges, these sister taxa are bathymetrically segregated. The hypothesis that black rockfish population genetic structure would resemble that of yellowtail rockfish was partially supported by this study. Both mitochondrial and microsatellite genetic structure shows discontinuities in similar regions of California near Cape Mendocino. These data, as well as a previous study (Seeb and Seeb 2005), support northern range expansion. However, black rockfish did not have a substantially higher degree of population structuring based on FST as might be expected given a preference for shallower depths as compared to yellowtail rockfish. Black rockfish may, however, be more prone to extinction and recolonization events resulting in localized genetic differentiation between neighboring collections to a degree not observed in yellowtail rockfish.