Africa Gómez

The Monopolization Hypothesis and the dispersal-gene flow paradox in aquatic organisms

Many aquatic organisms rely on passive transport of resting stages for their dispersal. In this review, we provide evidence pointing to the high dispersal capacity of both animals (cladocerans, rotifers and bryozoans) and aquatic macrophytes inhabiting lentic habitats. This evidence includes direct observation of dispersal by vectors such as wind and waterfowl and the rapid colonization of new habitats. Such high dispersal capacity contrasts with the abundant evidence of pronounced genetic differentiation among neighbouring populations in many pond-dwelling organisms. We provide an overview of the potential mechanisms causing a discrepancy between high dispersal rates and reduced levels of gene flow. We argue that founder events combined with rapid local adaptation may underlie the striking patterns of genetic differentiation for neutral markers in many aquatic organisms. Rapid population growth and local adaptation upon colonization of a new habitat result in the effective monopolization of resources, yielding a strong priority effect. Once a population is locally adapted, the presence of a large resting propagule bank provides a powerful buffer against newly invading genotypes, so enhancing priority effects. Under this Monopolization Hypothesis, high genetic differentiation among nearby populations largely reflects founder events. Phylogeographic data support a scenario of low effective dispersal among populations and persistent effects of historical colonization in cyclical parthenogens. A comparison of patterns of gene flow in taxa with different life cycles suggests an important role of local adaptation in reducing gene flow among populations. We argue that patterns of regional genetic differentiation may often reflect historical colonization of new habitats rather than contemporary gene flow.

Refugia within Refugia: Patterns of Phylogeographic Concordance in the Iberian Peninsula

The Iberian Peninsula was one of the most important Pleistocene glacial refugia in Europe. A number of recent studies have documented the phylogeography of Iberian taxa and their relationship to more widely distributed species that expanded from this southern European refugium. We use a comparative approach to review the literature that challenges the paradigm of Iberia as a single refuge during Pleistocene glacial maxima and instead supports the occurrence of several Iberian refugia for a range of flora and fauna. Some patterns of phylogeo-graphic concordance were found between the refugial areas identified by different case studies and these broadly overlapped with previously recognized areas of high endemism in the Iberian Peninsula. Such patterns help to illustrate the internal complexity of the Iberian Peninsula as a glacial refugium, and show that for many species, populations with a high degree of genetic structure have existed throughout the Pleistocene. Importantly, the occurrence of these ‘refugia-within-refugia’ may confound the interpretation of phylogeographic patterns of European species, and can misleadingly support the occurrence of northern refugia. We discuss these and other consequences, especially when a limited number of samples from the southern Euro-pean refugia are used.

SPECIATION IN ANCIENT CRYPTIC SPECIES COMPLEXES: EVIDENCE FROM THE MOLECULAR PHYLOGENY OF BRACHIONUS PLICATILIS (ROTIFERA)

Abstract Continental lake‐dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nu‐cleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

Sex, parthenogenesis and genetic structure of rotifers: microsatellite analysis of contemporary and resting egg bank populations

Cyclically parthenogenetic rotifers are a valuable model for investigating the relationship between reproductive mode and population structure, although advances in this field have been hindered by low allozyme variability in these organisms. A high genotypic diversity is predicted after population establishment, which would be eroded by clonal selection during the parthenogenetic phase. The resting egg bank, produced sexually, is presumed to store high levels of genetic diversity, with subsequent effects on planktonic population structure. Here, we provide the first application of microsatellite markers to a rotifer planktonic population and its associated resting egg bank. Seven polymorphic microsatellite loci were screened in populations of the rotifer Brachionus plicatilis in a temporary pond to analyse: (i) the genetic structure of the resting egg bank; (ii) the changes in the genetic structure of rotifer populations during the parthenogenetic phase; and (iii) the population structure after its initiation from resting eggs. Microsatellites proved to be a useful tool for clone identification, revealing a surprisingly high clonal diversity in rotifer populations. The last sample in the parthenogenetic phase showed evidence of clonal selection, as indicated by a low observed clonal diversity and the appearance of linkage disequilibria. The resting egg bank, analysed comprehensively for the first time in any zooplankter, is in Hardy–Weinberg and linkage equilibrium, and contains a high genotypic diversity. Unexpectedly, the resting egg bank differed from the planktonic population in its allelic composition, suggesting that resting egg hatching is biased.

Phylogeography and regional endemism of a passively dispersing zooplankter: mitochondrial DNA variation in rotifer resting egg banks

We investigated the phylogeography of the salt water rotifer Brachionus plicatilis, a cyclical parthenogen with passive dispersal mechanisms, using resting eggs recovered from saline lake sediments. Individual resting eggs were obtained from a large selection of lakes which were representative of five endorheic basins and the chain of coastal ponds in the Iberian Peninsula. The novel use of resting eggs allows the integration of seasonal and annual variations as well as the impact of stochastic effects such as drift and local extinction. A 653 bp fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene was sequenced from 98 eggs. Our results revealed a deep phylogeographical structure in this species, with a division into two main lineages with distinct geographical distributions, which probably diverged at the beginning of the Pleistocene period. Most of the mitochondrial DNA haplotypes were restricted to single lakes. Nested clade analysis supported Early Pleistocene fragmentation of populations, low gene flow and some long–distance colonization. These conclusions contrast strongly with previous ideas on rotifer biogeography and this pattern is consistent with a recolonization of the Iberian Peninsula from two glacial refugia. The results provide new insights into the processes responsible for the genetic diversification of passive dispersers, a life–history trait typical of zooplanktonic biotas.

Ecological genetics of a cyclical parthenogen in temporary habitats

Populations of the rotifer Brachionus plicatilis inhabiting three temporary ponds in Torreblanca Marsh (Castellón, Spain) were regularly screened for allozyme variation, sexual reproduction levels and population densities during an annual cycle. Relevant ecological parameters in the ponds were also recorded. The electrophoretic survey of the three ponds (Poza Sur, Poza Norte and Canal Central) revealed a high level of overall genetic polymorphism in four marker loci, but only 13 multilocus genotypes were found. We classified clones into three clonal groups (SS, SM, L) characterized by unique arrays of alleles in the four marker loci, and significant differences in body shape and size. Clonal group succession took place in Poza Sur; SM clones occurring in spring, SS clones from spring to fall, and L clones from fall to spring. Despite the partial overlapping of sexual periods, the absence of heterozygotes indicates that gene flow is strongly restricted between clonal groups. In the transition periods, the population was far from Hardy—Weinberg equilibrium due to hetereozygote deficiencies in all four markers. In clonal group L, the only polymorphic locus, Pgi, was in Hardy—Weinberg equilibrium. In clonal group SM, both polymorphic loci were in Hardy—Weinberg equilibrium in Poza Norte, but not in Poza Sur. Factor analysis on the limnological parameters recorded during field sampling indicates that genetically different clonal groups are also ecologically specialized. These findings suggest that the taxonomical species B. plicatilis is in fact a species complex. The complete genetic discontinuity model of rotifer population succession is supported by these data. Our results are similar to those found in cladocerans inhabiting temporary habitats.

Mating trials validate the use of DNA barcoding to reveal cryptic speciation of a marine bryozoan taxon.

Despite increasing threats to the marine environment, only a fraction of the biodiversity of the oceans has been described, owing in part to the widespread occurrence of cryptic species. DNA-based barcoding through screening of an orthologous reference gene has been proposed as a powerful tool to uncover biological diversity in the face of dwindling taxonomic expertise and the limitations of traditional species identification. Although DNA barcoding should be particularly useful in the sea, given the prevalence of marine cryptic species, the link between taxa identified through DNA barcodes and reproductively isolated taxa (biological species) has rarely been explicitly tested. Here, we use an integrated framework comparing breeding compatibility, morphology and mitochondrial (cytochrome c oxidase 1) and nuclear (elongation factor-1-alpha) DNA sequence variation among globally distributed samples of the cosmopolitan marine bryozoan Celleporella hyalina (L.). Our results reveal that C. hyalina comprises numerous deep, mostly allopatric, genetic lineages that are reproductively isolated, yet share very similar morphology, indicating rampant cryptic speciation. The close correspondence between genetic lineages and reproductively isolated taxa in the context of minimal morphological change suggests that DNA barcoding will play a leading role in uncovering the hidden biodiversity of the oceans and that the sole use of morphologically based taxonomy would grossly underestimate the number of marine species.

Phylogeography and local endemism of the native Mediterranean brine shrimp Artemia salina (Branchiopoda: Anostraca)

There has been a recent appreciation of the ecological impacts of zooplanktonic species invasions. The North American brine shrimp Artemia franciscana is one such alien invader in hyper‐saline water ecosystems at a global scale. It has been shown to outcompete native Artemia species, leading to their local extinction. We used partial sequences of the mitochondrial Cytochrome c Oxidase Subunit 1 (COI or cox1) gene to investigate the genetic diversity and phylogeography of A. salina, an extreme halophilic sexual brine shrimp, over its known distribution range (Mediterranean Basin and South Africa) and to assess the extent of local endemism, the degree of population structure and the potential impact of traditional human saltpan management on this species. We also examined the phylogenetic relationships in the genus Artemia using COI sequences. Our results show extensive regional endemism and indicate an early Pleistocene expansion of A. salina in the Mediterranean Basin. Subsequent population isolation in a mosaic of Pleistocene refugia is suggested, with two or three refugia located in the Iberian Peninsula. Two instances of long‐distance colonization were also observed. Surprisingly, given its strong phylogeographical structure, A. salina showed a signature of correlation between geographical and genetic distance. Owing to strong ‘priority effects’, extensive population differentiation is retained, despite dispersal via migrant birds and human management of saltpans. The foreseeable expansion of A. franciscana is likely to be followed by substantial loss of genetic diversity in Mediterranean A. salina. Large genetic divergences between Mediterranean and South African A. salina suggest that the latter deserves species status.

The interplay between colonization history and gene flow in passively dispersing zooplankton: microsatellite analysis of rotifer resting egg banks

Zooplanktonic organisms that disperse passively as diapausing eggs often exhibit surprisingly strong population subdivision given their high colonization ability. Here we attempt to disentangle the impacts of colonization history and gene flow on these organisms by studying the population genetic structure of the rotifer Brachionus plicatilis. The resting egg banks of B. plicatilis in fourteen salt lake populations in the Iberian Peninsula were examined using seven microsatellite loci. A remarkably high degree of geographical structuring was found (Fst=0.43), with a significant pattern of isolation by distance. Microsatellite loci were in genetic equilibrium, ruling out inbreeding as an important force in population structuring. Comparisons are drawn with previously published phylogeographical data. Surprisingly, introgression of nuclear genes was detected in neighbouring populations with divergent mtDNA haplotypes. These results stress the long lasting impact of colonization history and the modulating effect of gene flow at local scales in these organisms.

Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula

Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between observed cosmopolitanism in the zooplankton that is associated with long‐distance dispersal, and strong phylogeographical structures at a regional scale. Such population dynamics, far from migration–drift equilibrium, have been shown in the rotifer species complex Brachionus plicatilis, a group of over a dozen species inhabiting salt lakes and coastal lagoons worldwide. Here we present the mitochondrial DNA phylogeography of one of these species, Brachionus manjavacas, in the Iberian Peninsula, where it often co‐occurs with the morphologically similar species B. plicatilis sensu stricto. We obtained sequences from 233 individuals from diapausing eggs and clonal cultures from 16 lakes in the Iberian Peninsula, and a Tunisian lake. Two strongly supported deep mitochondrial DNA clades were found (A and B). Phylogenetic and nested clade analysis showed that clade A has a strong phylogeographical structure, with a strong similarity of phylogeographical patterns between B. manjavacas clade A and B. plicatilis s.s. These include (i) signatures of allopatric fragmentation between central and southern populations, and (ii) range expansions in the Iberian Peninsula, both likely to have occurred during the Pleistocene. We find evidence for a glacial refugium in the Guadiana basin. Clades A and B co‐occurred in several of these lakes because of range expansion and secondary contact between both clades. The co‐occurrence between B. plicatilis s.s. and B. manjavacas is not recent, and both species might have experienced similar environmental challenges during the Pleistocene. The strong correlation of genetic and geographical distance found suggests that historical events can lead to such correlation, mirroring the effects of ‘isolation by distance’ in equilibrium populations.