Sea (in)sight: from phylogeographical insights to visual local adaptation in marine gobies = (In)zicht op zee: van fylogeografische inzichten naar visuele lokale adaptatie bij mariene grondels

Exactly 150 years ago, Charles Darwin described natural selection as the motor of the evolution of life. Nevertheless, it is not yet clear how important natural selection is for the evolution of marine organisms.The genetic adaptation to local environmental conditions as a result of natural selection, a process known as local adaptation, will be reduced by the migration of organisms due to its homogeneous character. Because of the huge potential for migration in the ‘open’ sea, for a long time biologists declared that local adaptation is rare and even absent.Nevertheless, current research shows that the sea is not as ‘open’ as it may seem. Many marine organisms are able to occupy a permanent place and hence occur in distinct populations. Since migration seems limited, the possibility of local adaptation in marine species presents an important research question. The most recent studies showed that natural selection might be an important evolutionary force in the ocean, however without any good scientific evidence.The present thesis has the ambition to prove that marine species may indeed be genetically adapted to local conditions. A promising opportunity is the possibility for local adaptation to the light regime of the sea. The light that organisms perceive varies between seas due to the differences in turbidity and the colour of the water. The importance of sight for marine animals is obvious, especially to find food and mates, and to avoid predators. Therefore, the aim of the thesis was to study local adaptation at the rhodopsin gene - the gene of the visual pigment that determines the visual capacity in dim-light - of a marine goby, the sand goby (Pomatoschistus minutus). The sand goby is a small and abundant fish species that lives along the European coasts.The results showed strong evidence that sand goby populations are genetically adapted to their specific and local light environment. They are adapted to high turbidity in the Baltic Sea and the Mediterranean lagoons, and to the more blue light of the Bay of Biscay and along the coasts of Spain and Portugal. Moreover, the sand gobies of the North Sea reveal a strategy of adaptation to the unstable local light conditions. In the current state of science, the rhodopsin gene provides one of the strongest indications that local adaptation occurs in the marine environment. Therefore, they encourage analogous studies to find further evidence for l ocal adaptation to other marine environmental conditions such as salinity tolerance and temperature. Such studies will clarify the importance of natural selection as evolutionary force for marine life.To conclude, this study reveals that the sand goby is evolutionary adapted to its light environment. There are strong indications that if the light environment changes due to either pollution or climate change, marine fishes won’t likely be able to adapt rapidly to the new circumstances. Good management of the light conditions of the marine ecosystem will be essential to support a balanced ecosystem and healthy fish stocks

Signature of selection on the rhodopsin gene in the marine radiation of American seven-spined gobies (Gobiidae, Gobiosomatini)

In comparison with terrestrial and freshwater ecosystems, information about speciation modes and the role of selection in marine environments is scarce. Recent studies have indicated that spectral adaptation could play an important role in the diversification of marine species flocks. Natural selection influences specific amino acids (AAs) that are involved in the spectral tuning mechanism of visual pigment genes. To study the wider occurrence and the characteristics of spectral adaptation in marine radiations, a reinterpretation of the rhodopsin (RH1) data of American seven-spined gobies (genus Elacatinus; Gobiidae; Teleostei) was carried out. Reanalysis revealed that some AAs, which are well known in the literature as spectral tuning sites, are variable in Elacatinus. Those crucial AA substitutions originated polyphyletically, indicating convergent evolution within the genus Elacatinus. Moreover, statistical tests based on the dN/dS ratio detected selection in several phylogenetic lineages and at specific AAs. Many of these AAs were previously shown to be under selection in other marine radiations. Therefore, the current phylogenetic approach provided an extended list of AAs that are probably involved in spectral tuning, and which should be validated by mutagenic experiments

Exploring glacial and present evolutionary patterns of a marine goby, <i>Pomatoschistus minutus</i>

A classical understanding of marine fishes is that they have high effective population sizes and high levels of dispersal due to an apparent lack of barriers in the marine environment. The realization of a genetic population structure is therefore thought to be a slow process. To gain insights in this process, it is a challenge to disentangle the interaction between selection, gene flow, population history and genetic drift. The sand goby (Pomatoschistus minutus), which is an important ecological but noncommercial species, was chosen to distinguish between natural and anthropologically induced processes. A spatio-temporal analysis with samples from different localities throughout the species distribution and with two types of genetic markers was performed to assess the neutral genetic population structure. Phylogeographical patterns were studied by sequence cytochrome b (mtDNA). Nine new nuclear microsatellites were developed and used to describe the current genetic diversity and population structure. The genetic structure of the sand goby is best explained by a combination of present and historic factors. Due to its high potential for dispersion and high effective population size, it shows the typical features of a marine fish with a high level of diversity and a limited degree of genetic differentiation. The large genetic distance between the Venetian and all other samples shows that the sand gobies from the Adriatic Sea should be considered as a distinct cryptic species of the genus Pomatoschistus. Low but significant differentiation is observed between Atlantic and western Mediterranean P. minutus. In the Atlantic and Baltic basins, there is evidence for a postglacial range expansion and a weak pattern of isolation-by-distance. Furthermore the results support the hypothesis of a glacial refugium and a fine-scale genetic structure in the southern North Sea. The neutral genetic pattern will be compared with putatively adaptive loci in order to study the genomic characteristics of local adaptation in the marine environment. This should provide a better understanding of how fish respond to changes in the environment

Deep genetic divergence and recent radiations in sand goby <i>Pomatoschistus minutus</i> along European coasts

Understanding evolutionary patterns is more complex in marine compared to continental species because marine species have high effective population sizes and high levels of dispersal due to an apparent lack of barriers. Moreover, phylogeographical breaks in the marine realm such as the Atlantic-Mediterranean transition remain controversial. Therefore a new high-quality phylogeographic analysis was realized for a marine demersal fish, the sand goby Pomatoschistus minutus (Gobiidae, Teleostei). Sand gobies of 12 locations along the full European distribution range were analyzed by sequencing a large fragment of the mitochondrial cytochrome b gene.The phylogenetic results show that P. minutus comprises two deep genealogical lineages, the Mediterranean Sea Clade (MS-Clade) and the Atlantic Ocean Clade (AOClade), that date back to the Early Pleistocene (1.6-0.8 MYA). Even though the sand goby occurs only in a few northern locations in the Mediterranean, the MS-Clade contains the Significant Units (ESU), one off the Western Iberian Peninsula and the other in the marine systems of the North Atlantic (Bay of Biscay, North Sea, Irish Sea and Baltic Sea). This is consistent with two separate palaeorefugia during the Pleistocene glaciations: the Iberian Peninsula and the Bay of Biscay. Less haplotypes were shared among the marine systems of the North Atlantic, indicating a low present-day gene flow. The network analysis showed a recent radiation in each marine system, even in the northern Baltic Sea where the recolonization of P. minutus occurred only 8000 years ago. This phylogeographic pattern will be compared with putatively adaptive loci in order to study the characteristics of local adaptation in the marine environment

The Dutch Y-chromosomal landscape

Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic-geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.Molecular Technology and Informatics for Personalised Medicine and Healt

Identification and characterization of novel rapidly mutating Y-chromosomal short tandem repeat markers

Short tandem repeat polymorphisms on the male‐specific part of the human Y‐chromosome (Y‐STRs) are valuable tools in many areas of human genetics. Although their paternal inheritance and moderate mutation rate (~10−3 mutations per marker per meiosis) allow detecting paternal relationships, they typically fail to separate male relatives. Previously, we identified 13 Y‐STR markers with untypically high mutation rates (>10−2 ), termed rapidly mutating (RM) Y‐STRs, and showed that they improved male relative differentiation over standard Y‐STRs. By applying a newly developed in silico search approach to the Y‐chromosome reference sequence, we identified 27 novel RM Y‐STR candidates. Genotyping them in 1,616 DNA‐confirmed father–son pairs for mutation rate estimation empirically highlighted 12 novel RM Y‐STRs. Their capacity to differentiate males related by 1, 2, and 3 meioses was 27%, 47%, and 61%, respectively, while for all 25 currently known RM Y‐STRs, it was 44%, 69%, and 83%. Of the 647 Y‐STR mutations o

Development and characterization of nine polymorphic microsatellite markers in the sand goby <i>Pomatoschistus minutus</i> (Gobiidae)

A microsatellite-enriched genomic library was constructed for the sand goby, Pomatoschistus minutus (Pallas 1770), and nine polymorphic DNA microsatellite markers of high quality were successfully optimized. Characterization of 96 individuals from the Vaccarès lagoon (France) showed moderate to high levels of polymorphism (two to 54 alleles). All the markers conformed to Hardy-Weinberg equilibrium and showed no evidence of null alleles, large allele dropout, stuttering and linkage disequilibrium between pairs of loci. These markers successfully amplify in three closely related species and can be employed to investigate population genetic structure and to clarify paternity in Pomatoschistus species

Mito-nuclear discordance in the degree of population differentiation in a marine goby

An increasing number of phylogeographic studies on marine species shows discordant patterns in the degree of population differentiation between nuclear and mitochondrial markers. To understand better which factors have the potential to cause these patterns of discordance in marine organisms, a population genetic study was realized on the sand goby Pomatoschistus minutus (Pallas 1770; Gobiidae, Teleostei). Sand gobies from eight European locations were genotyped at eight microsatellite markers. Microsatellites confirmed the global phylogeographical pattern of P. minutus observed with mitochondrial DNA (mtDNA) markers and nuclear allozyme markers. Three groups consistent with the mitochondrial lineages were defined (the Mediterranean, Iberian and North Atlantic groups) and indications of a recent founder event in the northern Baltic Sea were found. Nevertheless, differences in the degree of population differentiation between the nuclear and mitochondrial markers were large (global FST-values for microsatellites=0.0121; for allozymes=0.00831; for mtDNA=0.4293). Selection, sex-biased dispersal, homoplasy and a high effective population size are generally accepted as explanations for this mitonuclear discrepancy in the degree of population differentiation. In this study, selection on mtDNA and microsatellites, male-biased dispersal and homoplasy on microsatellite markers are unlikely to be a main cause for this discrepancy. The most likely reason for the discordant pattern is a recent demographical expansion of the sand goby, resulting in high effective population sizes slowing down the differentiation of nuclear DNA