Phylogeography of Supralittoral Rocky Intertidal Ligia Isopods in the Pacific Region from Central California to Central Mexico

Background

Ligia isopods are widely distributed in the Pacific rocky intertidal shores from central California to central Mexico, including the Gulf of California. Yet, their biological characteristics restrict them to complete their life cycles in a very narrow range of the rocky intertidal supralittoral. Herein, we examine phylogeographic patterns of Ligia isopods from 122 localities between central California and central Mexico. We expect to find high levels of allopatric diversity. In addition, we expect the phylogeographic patterns to show signatures of past vicariant events that occurred in this geologically dynamic region.

Methodology/Principal Findings

We sequenced two mitochondrial genes (Cytochrome Oxidase I and 16S ribosomal DNA). We conducted Maximum Likelihood and Bayesian phylogenetic analyses. We found many divergent clades that, in general, group according to geography. Some of the most striking features of the Ligia phylogeographic pattern include: (1) deep mid-peninsular phylogeographic breaks on the Pacific and Gulf sides of Baja peninsula; (2) within the Gulf lineages, the northern peninsula is most closely related to the northern mainland, while the southern peninsula is most closely related to the central-southern mainland; and, (3) the southernmost portion of the peninsula (Cape Region) is most closely related to the southernmost portion of mainland.

Conclusions/Significance

Our results shed light on the phylogenetic relationships of Ligia populations in the study area. This study probably represents the finest-scale phylogeographic examination for any organism to date in this region. Presence of highly divergent lineages suggests multiple Ligia species exist in this region. The phylogeographic patterns of Ligia in the Gulf of California and Baja peninsula are incongruent with a widely accepted vicariant scenario among phylogeographers, but consistent with aspects of alternative geological hypotheses and phylo- and biogeographic patterns of several other taxa. Our findings contribute to the ongoing debate regarding the geological origin of this important biogeographic region.     

Assessing Posidonia oceanica Seedling Substrate Preference: An Experimental Determination of Seedling Anchorage Success in Rocky vs. Sandy Substrates

In the last decades the growing awareness of the ecological importance of seagrass meadows has prompted increasing efforts to protect existing beds and restore degraded habitats. An in-depth knowledge of factors acting as major drivers of propagule settlement and recruitment is required in order to understand patterns of seagrass colonization and recovery and to inform appropriate management and conservation strategies. In this work Posidonia oceanica seedlings were reared for five months in a land-based culture facility under simulated natural hydrodynamic conditions to identify suitable substrates for seedling anchorage. Two main substrate features were investigated: firmness (i.e., sand vs. rock) and complexity (i.e., size of interstitial spaces between rocks). Seedlings were successfully grown in culture tanks, obtaining overall seedling survival of 93%. Anchorage was strongly influenced by substrate firmness and took place only on rocks, where it was as high as 89%. Anchorage occurred through adhesion by sticky root hairs. The minimum force required to dislodge plantlets attached to rocky substrates reached 23.830 N (equivalent to 2.43 kg), which would potentially allow many plantlets to overcome winter storms in the field. The ability of rocky substrates to retain seedlings increased with their complexity. The interstitial spaces between rocks provided appropriate microsites for seedling settlement, as seeds were successfully retained, and a suitable substrate for anchorage was available. In conclusion P. oceanica juveniles showed a clear-cut preference for hard substrates over the sandy one, due to the root system adhesive properties. In particular, firm and complex substrates allowed for propagule early and strong anchorage, enhancing persistence and establishment probabilities. Seedling substrate preference documented here leads to expect a more successful sexual recruitment on hard bottoms compared with soft ones. This feature could have influenced P. oceanica patterns of colonization in past and present time.     

A Complex Evolutionary History in a Remote Archipelago: Phylogeography and Morphometrics of the Hawaiian Endemic Ligia Isopods

Compared to the striking diversification and levels of endemism observed in many terrestrial groups within the Hawaiian Archipelago, marine invertebrates exhibit remarkably lower rates of endemism and diversification. Supralittoral invertebrates restricted to specific coastal patchy habitats, however, have the potential for high levels of allopatric diversification. This is the case of Ligia isopods endemic to the Hawaiian Archipelago, which most likely arose from a rocky supralittoral ancestor that colonized the archipelago via rafting, and diversified into rocky supralittoral and inland lineages. A previous study on populations of this isopod from Oʻahu and Kauaʻi revealed high levels of allopatric differentiation, and suggested inter-island historical dispersal events have been rare. To gain a better understanding on the diversity and evolution of this group, we expanded prior phylogeographic work by incorporating populations from unsampled main Hawaiian Islands (Maui, Molokaʻi, Lanaʻi, and Hawaiʻi), increasing the number of gene markers (four mitochondrial and two nuclear genes), and conducting Maximum likelihood and Bayesian phylogenetic analyses. Our study revealed new lineages and expanded the distribution range of several lineages. The phylogeographic patterns of Ligia in the study area are complex, with Hawaiʻi, Oʻahu, and the Maui-Nui islands sharing major lineages, implying multiple inter-island historical dispersal events. In contrast, the oldest and most geographically distant of the major islands (Kauaʻi) shares no lineages with the other islands. Our results did not support the monophyly of all the supralittoral lineages (currently grouped into L. hawaiensis), or the monophyly of the terrestrial lineages (currently grouped into L. perkinsi), implying more than one evolutionary transition between coastal and inland forms. Geometric-morphometric analyses of three supralittoral clades revealed significant body shape differences among them. A taxonomic revision of Hawaiian Ligia is warranted. Our results are relevant for the protection of biodiversity found in an environment subject to high pressure from disturbances.     

Chloroplast DNA Phylogeography Reveals Repeated Range Expansion in a Widespread Aquatic Herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and Adjacent Areas

Background

The Qinghai-Tibetan Plateau (QTP) is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown.

Methodology and Principal Findings

We studied the phylogeography and demographic history of the widespread aquatic herb Hippuris vulgaris from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of H. vulgaris. Using sequences from four chloroplast DNA (cpDNA) non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in H. vulgaris, we found a very high level of population differentiation (G _ST = 0.819) but the phylogeographical structure remained obscure (N _ST = 0.853>G _ST = 0.819, P>0.05). Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr). Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr) might have begun from the different refugees before the Last Glacial Maximum (LGM).

Conclusions/Significance

This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations.     

Contrasting clonal structure among Pocillopora (Scleractinia) communities at two environmentally distinct sites in the Gulf of California

The contributions of sexual versus asexual reproduction are thought to play an important role in the abundance and ecological success of corals, especially in marginal habitats. Pocillopora corals are distributed throughout the Indo-Pacific and dominate shallow hard-bottom communities in the eastern Pacific where broad seasonal fluctuations in temperature and water turbidity create suboptimal conditions for reef community development. Previous work had revealed three genetic clades in the eastern Pacific that show little correspondence with colony morphology; the broad distribution of type 1 extends into the subtropical southern Gulf of California. Here we examine genetic and clonal structure of two type 1 communities separated by 10?km with microsatellite data. Samples were collected randomly in six 10 m radius circular plots (20 colonies per plot, 3 plots per site). Sites differed in their relative clonality because clonemates (ramets) from a single clone (genet) dominated a large portion (90.9?m long) of the protected leeward side of Gaviota Island (Number of genets/Number of samples?=?0.35; observed Genotypic diversity/expected Genotypic diversity?=?0.087), while an exposed community at the entrance to La Paz Bay, Punta Galeras, exhibited high genotypic diversity (N _g /N?=?0.85; G _o /G _e ?=?0.714). Gene flow was unrestricted between sites indicating these communities comprised a single population. The relative proportion of asexual colonies found between community aggregations of Pocillopora in the Gulf of California differed significantly and suggests factors at local, not regional, scales affect these patterns. The possibility that heterogeneity in clonal structure is common throughout the eastern Pacific and across the west Indo-Pacific requires further study. Finally, since morphological variation in Pocillopora has been underappreciated and is in need of taxonomic revision, the use of a consistent field-sampling protocol and high-resolution makers will advance ecological research and aid in the conservation of these corals.     

青藏高原及其周边地区高山植物谱系地理学研究进展

青藏高原及其周边地区是世界上高山植物最丰富的地区,通过谱系地理学研究可以探讨高山植物演化历史与高原隆升和第四纪冰期的关系。根据对已经报道的36种高山植物的谱系地理分析,其谱系地理模式主要表现为:一、冰期退却到高原边缘的避难所,冰后期回迁到高原面;二、地理隔离造成冰期存在多处避难所(含微型避难所),冰后期发生局域性扩张。青藏高原在晚第三纪的快速隆升促进了物种的分化和成种,而第四纪冰期更是加剧了物种的快速分化,高原隆升和第四纪周期性气候波动是形成青藏高原高山植物现代谱系地理格局的主要原因。横断山脉地区作为第四纪冰期高山植物的主要避难所,在进化生物学和保护生物学方面具有重要启示。最后在物种选择、采样策略、基因片段选择和研究方法等4个方面提出青藏高原地区谱系地理学的研究方向。     

Hepatic carcinoma with spleen metastasis in a California sea lion from the Gulf of California.

A primary hepatic carcinoma with a neuroendocrine pattern was detected in an adult female California sea lion (Zalophus californianus) found dead on Granito Island in the Gulf of California (Mexico) in January 1996. At necropsy, several light yellow nodules of different sizes were observed on the entire surface of the liver and spleen. Microscopic examination of these nodules using routine haematoxylin-eosin stain, revealed cubic, polyhedral and pleomorphic cells with three to four bizarre mitotic figures per field (40X). An immunohistochemistry test revealed a positive reaction of indirect immunoperoxide to cytokeratin (CK2). This is the first known case of a primary hepatic carcinoma in free-ranging California sea lions from Mexican waters.     

Fish larvae assemblages in the Gulf of California

The distributional diversity and assemblages of fish larvae in the Gulf of California indicated two main seasonal stages and two transitional periods: in winter, the tropical water mass is confined to the south‐east portion of the mouth of the Gulf and larval fish assemblages are dominated by subtropical and temperate‐subarctic species; in summer; tropical water invades the Gulf and assemblages are dominated by tropical species. Both seasonal stages are separated by transitional periods coinciding with strong latitudinal temperature gradients. During the autumn and spring transitional periods, the Gulf of California splits into three regions: a northern region where temperate and subarctic species spawn from autumn to spring, a southern region dominated by tropical and subtropical species year round and a central region where tropical and temperate assemblages merge. Seasonal changes in the location of the regions, as well as the borders between them, show expansion and contraction of the northern and southern faunas related to the general oceanic circulation patterns during the year.     

Ecological effects of seaweed harvesting in the Gulf of California and Pacific Ocean off Baja California and California

The ecological effects of harvesting were investigated for two species, the giant kelp Macrocystis pyrifera and Eucheuma uncinatum, by using harvest records and aerial surveys that show yield changes and by using studies of recruitment, survivorship and community interactions. There were no ecological effects found for M. pyrifera harvested with contemporary methods, and there are no recommendations for changing current management practices for this species. It is recommended that E. uncinatum, which on occasion produces commercially significant standing crops, not be harvested unless special precautions are taken to leave some plants for regeneration of the harvested populations.     

Phylogeography and introgressive hybridization: chipmunks (genus Tamias) in the northern Rocky Mountains

Abstract. If phylogeographic studies are to be broadly used for assessing population-level processes relevant to speciation and systematics, the ability to identify and incorporate instances of hybridization into the analytical framework is essential. Here, we examine the evolutionary history of two chipmunk species, Tamias ruficaudus and Tamias amoenus , in the northern Rocky Mountains by integrating multivariate morphometrics of bacular (os penis) variation, phylogenetic estimation, and nested clade analysis with regional biogeography. Our results indicate multiple examples of mitochondrial DNA introgression layered within the evolutionary history of these nonsister species. Three of these events are most consistent with recent and/or ongoing asymmetric introgression of mitochondrial DNA across morphologically defined secondary contact zones. In addition, we find preliminary evidence where a fourth instance of nonconcordant characters may represent complete fixation of introgressed mitochondrial DNA via a more ancient hybridization event, although alternative explanations of convergence or incomplete sorting of ancestral polymorphisms cannot be dismissed with these data. The demonstration of hybridization among chipmunks with strongly differentiated bacular morphology contradicts long-standing assumptions that variation within this character is diagnostic of complete reproductive isolation within Tamias . Our results illustrate the utility of phylogeographic analyses for detecting instances of reticulate evolution and for incorporating this and other information in the inference of the evolutionary history of species.     

Evidence of Leptospira interrogans infection in California sea lion pups from the Gulf of California

Forty-two urine and 96 blood and serum samples were obtained from California sea lion (Zalophus californianus) pups from the Gulf of California during the 2000 reproductive season. Antibody prevalence to 13 serovars of Leptospira interrogans was determined by microagglutination tests (MAT); presence of pathogenic leptospires was detected by polymerase chain reaction (PCR). Samples with antibody titers > or = 1:25 or 115 bp fragments on ethidium bromidestained 1.5% agarose gels were considered positive. Antibody prevalence was 54% overall with highest prevalence against serovar cynopteri (50% of all positive reactions). Highest antibody titers (1:50) were detected against serovars cynopteri and pomona. Polymerase chain reaction products were observed in two of 42 urine samples, six of 96 blood samples, and one of 96 serum samples. Presence of PCR products in blood and serum was demonstrated in pups that were seronegative. Kruskall-Wallis tests and corresponding post hoc Tukey tests (alpha = 0.05) showed that prevalence of leptospirosis was significantly different among all rookeries. The high seroprevalence (54%), low antibody titers (maximum 1:50), absence of pups showing clinical signs indicative of the disease, and lack of recent reports of increased mortality of sea lions in the Gulf of California are suggestive of the presence of enzootic host-adapted serovars. Crowding in rookeries as well as the presence of bats and rodents on some of the islands may explain infection by L. interrogans (sensu lato) and some of the differences in seroprevalence among reproductive rookeries.     

Plankton response to physical forcing in the Gulf of California

Distinct increases in plankton productivity occur annually inthe Gulf of California and are related, at least in part, towind-driven changes in upper-ocean conditions. In particular,a rapid increase in plankton shell fluxes occurs in late fall(November), and is associated with a shift to northerly windsand cooling of surface temperatures that induce mixing of theupper ocean. The observed succession in the phytoplankton isattributed to this destabilization of surface waters and mayreflect the ability of different groups to rapond to varyingsurface water nutrient levels. The unraveling of such relationshipsbetween plankton production and hydrographic conditions is criticalto improving our ability to reconstruct quantitatively pastclimates.     

Species composition and morphologic variation of Porites in the Gulf of California

Morphometric analysis of corallite calices confirmed that from the late Miocene to the Recent, four species of Porites have inhabited the Gulf of California: the extinct Porites carrizensis, the locally extirpated Porites lobata and the extant Porites sverdrupi and Porites panamensis. Furthermore, large-scale spatial and temporal phenotypic plasticity was observed in the dominant species P. panamensis. Canonical discriminant analysis and ANOVA demonstrated that the calice structures of P. panamensis experienced size reduction between the late Pleistocene and Recent. Similarly, PERMANOVA, regression and correlation analyses demonstrated that across the 800 km north to south in the gulf, P. panamensis populations displayed a similar reduction in calice structures. Based on correlation analysis with environmental data, these large spatial changes are likely related to changes in nutrient concentration and sea surface temperature. As such, the large-scale spatial and temporal phenotypic variation recorded in populations of P. panamensis in the Gulf of California is likely related to optimization of corallite performance (energy acquisition) within various environmental scenarios. These findings may have relevance to modern conservation efforts within this ecological dominant genus.     

青藏高原及其毗邻山区蒙古绣线菊谱系地理学研究

以青藏高原及其毗邻山区的蒙古绣线菊23个居群324个个体为研究对象,选取叶绿体DNA非编码区trnL-trnF和rps15-ycf1片段对蒙古绣线菊进行谱系地理学研究。结果表明:(1)该研究区域中蒙古绣线菊亲缘关系相近的单倍型多发生于同一居群中,存在着明显的谱系地理学关系。(2)所检测得到的35个单倍型中,大约71.4%是居群内特有的单倍型,而出现频率最高的H1是最古老的单倍型,贝叶斯分析和单倍型简约网状图显示35个单倍型聚为地理分布范围各不相同的3个分支。(3)歧点分布分析得到分布图呈多峰曲线,说明蒙古绣线菊居群在较长的时间内发展稳定,没有经历突然的近期扩张。(4)BEAST分析结果显示,在45Mya左右开始出现蒙古绣线菊的谱系分支的分化。研究认为,蒙古绣线菊在青藏高原及其毗邻山区可能至少存在3个冰期避难所,其在青藏高原及其毗邻山区的分布格局主要是第四纪冰期-间冰期气候动荡、青藏高原隆升的共同作用的结果。     

Intraspecific Phylogeography of Red Squirrels (Tamiasciurus hudsonicus) in the Central Rocky Mountain Region of North America

We used variation in a portion of the mitochondrial DNA control region to examine phylogeography of Tamiasciurus hudsonicus, a boreal-adapted small mammal in the central Rocky Mountain region. AMOVA revealed that 65.66% of genetic diversity was attributable to variation within populations, 16.93% to variation among populations on different mountain ranges, and 17.41% to variation among populations within mountain ranges. Nested clade analysis revealed two major clades that likely diverged in allopatry during the Pleistocene: a southern clade from southern Colorado and a northern clade comprising northern Colorado, Wyoming, eastern Utah, and eastern Idaho. Historically restricted gene flow as a result of geographic barriers was indicated between populations on opposite sides of the Green River and Wyoming Basin and among populations in eastern Wyoming. In some instances genetic structure indicated isolation by distance.     

Aspects of Nutrition and the Metabolism of Copper in Isopods

Terrestrial immigrants from the sea have to cope with two importantnutritional problems: a shift in pathways of absorption, andthe altered availability of nutrients. The more terrestrialspecies of littoral crustaceans switch to food as the main sourceof water and salts. No serious difficulties accompany the oraluptake of mobile ions, but the vegetarians amongst the immigrantsare required to assume a new attitude with regard to the assimilationor heavier metals. Some important heavy elements, notably Cuand Zn, are soluble in sea water but form rather intractableorganic complexes in plant tissues. Herbivorous amphipods andisopods on land are incapable of extracting copper directlyfrom their primary food sources. To compensate for this shortcoming,help is enlisted from microorganisms, which render the copperpresent in ill-digested fecal material available to the crustaceans.Moreover, in terrestrial and intertidal herbivorous crustaceans—ascompared with their marine relatives—the storage capacityof the hepatopancreas, as well as the efficiency of Cu-assimilation,is augmented; compartmentalization of Cu-storage is more rigorouslycarried through; the movements of Cu and Zn within the bodyare more strictly regulated, copper, for example, being exchangedbetween different compartments in the course of endogenouslyor exogenously induced phases of the animal's life cycle.     

Desiccation,predation, and mussel-barnacle interactions in the northern Gulf of California

Summary Field experiments were conducted in order to determine the potential for desiccation and predation to mediate the effect of mussels (Brachidontes semilaevis) on barnacles (Chthamalus anisopoma) in the highly seasonal northern Gulf of California. We did this by removing both mussels and a common mussel predator (Morula ferruginosa: Gastropoda) and by spraying selected sites with sea water during summertime spring low tides. We also determined the effect of crowding on resistance to desiccation in barnacles, and the effect of barnacles on colonization by mussels. The mussel-barnacle community was not affected by keeping experimental quadrats damp during daytime low tides throughout the summer. Exposure to summertime low tides, however, did affect the survivorship of isolated, but not crowded, barnacles; and barnacle clumps enhanced the recruitment of mussels. Hence crowding in barnacles had a positive effect on both barnacle survivorship and mussel recruitment. Morula had a negative effect on mussel density, and mussels had a negative effect on barnacle density. The effect of Morula on barnacle density was positive, presumably due to its selective removal of mussels. These results suggest an indirect mutualism between barnacles and the gastropod predator, because barnacles attract settlement or enhance the survival of mussels, and the predator reduces the competitive effect of mussels on barnacles.     

Phylogeography of sugar kelp: Northern ice‐age refugia in the Gulf of Alaska

Many Northeast (NE) Pacific fishes and invertebrates survived Pleistocene glaciations in northern refugia, but the extent that kelps survived in northern areas is uncertain. Here, we test the hypothesis that populations of sugar kelp (Saccharina latissima) persisted in the Gulf of Alaska during ice‐age maxima when the western margin of the Cordilleran ice sheet covered coastal areas around the NE Pacific Ocean. We estimated genetic diversities within and phylogeographical relationships among 14 populations along 2,800 km in the NE Pacific and Bering Sea with partial sequences of mitochondrial DNA 5′‐cytochrome oxidase subunit I (COI, bp = 624, n = 543), chloroplast DNA ribulose‐1,5‐bisphosphate carboxylase large subunit‐3′ (rbcL, bp = 735, n = 514), and 11 microsatellite loci. Concatenated sequences of rbcL and COI showed moderate levels of within‐population genetic diversity (mean h = 0.200) but substantial differences among populations (Φ_ST = 0.834, p < .0001). Microsatellites showed moderate levels of heterozygosity within populations (mean H _E = 0.391). Kelps in the same organellar lineage tended to cluster together, regardless of geographic origins, as indicated in a principal coordinate analysis (PCoA) of microsatellite genotypes. The PCoA also showed evidence of nuclear hybridizations between co‐occurring organellar lineages. Individual admixture plots with population clusters of K = 2, 6, and 9 showed increasing complexity with considerable historical admixture between some clusters. A time‐calibrated phylogeny placed divergences between rbcL‐COI lineages at 1.4 million years at most. The time frames of mutation in the rbcL‐COI lineages and microsatellite population clusters differed among locations. The existence of ancient lineages in the Gulf of Alaska, moderate levels of genetic diversity, and the absence of departures from neutrality are consistent with northern refugia during multiple Croll‐Milankovitch climate cycles in the Pleistocene Epoch.     

Cryptic vicariance in Gulf of California fishes parallels vicariant patterns found in Baja California mammals and reptiles

Comparisons across multiple taxa can often clarify the histories of biogeographic regions. In particular, historic barriers to movement should have affected multiple species and, thus, result in a pattern of concordant intraspecific genetic divisions among species. A striking example of such comparative phylogeography is the recent observation that populations of many small mammals and reptiles living on the Baja California peninsula have a large genetic break between northern and southern peninsular populations. In the present study, I demonstrate that five species of near-shore fishes living on the Baja coastline of the Gulf of California share this genetic pattern. The simplest explanation for this concordant genetic division within both terrestrial and marine vertebrates is that the Baja Peninsula was fragmented by a Plio-Pleistocene marine seaway and that this seaway posed a substantial barrier to movement for near-shore fishes. For some fish species, the signal of this vicariance in mtDNA has been eroded by gene flow and is not evident with classic, equilibrium measures of population structure. Yet, significant divisions are apparent in coalescent analyses that jointly estimate divergence with gene flow. The genetic divisions within Gulf of California fishes also coincide with recognized biogeographic regions based on fish community composition and several environmental factors. It is likely that adaptation to regional environments and present-day oceanographic circulation limit gene exchange between biogeographic regions and help maintain evidence of past vicariance.