Article

Diversification in gravel beaches: A radiation of interstitial clingfish (Gouania, Gobiesocidae) in the Mediterranean Sea

Authors:
  • Meersschule Pula, Morska Skola
  • Natural History Museum Rijeka
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... Above all, many cryptobenthic taxa contain morphologically similar or, at least at first glance, identical species, such that their overall biodiversity is drastically underestimated, even in considerably wellstudied groups or geographic regions (e.g., Conway et al., 2014;Tornabene et al., 2015;Wagner et al., 2019;Winterbottom et al., 2014). However, the inclusion of molecular methods in classic taxonomic studies has proven to be particularly effective for overcoming these obstacles and in recent years genetic data have become a key tool for resolving phylogenetic relationships among and within cryptobenthic taxa (e.g., Almada et al., 2008;Conway et al., 2014;Henriques et al., 2002;Hoban & Williams, 2020;Kovači c et al., 2020;Tornabene et al., 2010;Victor, 2013;Winterbottom et al., 2014). ...
... From the Mediterranean Sea, nine species in six genera have been described and almost all of them exclusively inhabit upper littoral ecosystems (Bileceno glu et al., 2017;Hofrichter & Patzner, 2000). One of them, Gouania willdenowi (Risso 1810), the only described species of the genus Gouania Nardo, 1833, has stenoeciously adapted to life in the interstitial of Mediterranean intertidal gravel beaches (Hofrichter & Patzner, 2000;Wagner et al., 2019). The narrow interstitial space of intertidal gravel beaches is characterized by extreme mechanical (shearing forces) and tidal stressors (e.g., daily desiccation) and can be considered as one of the most demanding environments for fishes (see Supporting Information Video S1 for behavioural observation). ...
... The narrow interstitial space of intertidal gravel beaches is characterized by extreme mechanical (shearing forces) and tidal stressors (e.g., daily desiccation) and can be considered as one of the most demanding environments for fishes (see Supporting Information Video S1 for behavioural observation). Indeed, among all known fishes, only Gouania and some Pacific gobies of the genus Luciogobius Gill, 1859 have evolved adaptations to live in this particular environment (Wagner et al., 2019;Yamada et al., 2009). ...
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The clingfish (Gobiesocidae) genus Gouania (Nardo 1833) is endemic to the Mediterranean Sea and inhabits, unlike any other vertebrate species in Europe, the harsh intertidal environment of gravel beaches. Following up on a previous phylogenetic study, we revise the diversity and taxonomy of this genus, by analysing a comprehensive set of morphological (meristics, morphometrics, micro computed tomography imaging), geographical and genetic (DNA‐barcoding) data. We provide descriptions of three new species, G. adriatica sp. nov., G. orientalis sp. nov., G. hofrichteri sp. nov. as well as re‐descriptions of G. willdenowi (Risso 1810) and G. pigra (Nardo 1827) and assign neotypes for the latter two species. In addition to elucidating the complex taxonomic situation of Gouania, we discuss the potential of this enigmatic clingfish genus for further ecological, evolutionary and biodiversity studies that might unravel even more diversity in this unique Mediterranean fish radiation.
... The term itself derives from the fact that they attach themselves to the substrate by means of a ventrally located adhesive disc (Briggs, 1955;Conway et al., 2017Conway et al., , 2019. Their unusual lifestyle and small body size explain why they are generally considered as cryptobenthic, which in turn suggests that clingfish biodiversity has been underestimated (Brandl et al., 2018;Wagner et al., 2019Wagner et al., , 2020. Within the Gobiesocidae, this applies in particular to the genus Gouania Risso 1810, which originally included only the species Gouania willdenowi. ...
... Within the Gobiesocidae, this applies in particular to the genus Gouania Risso 1810, which originally included only the species Gouania willdenowi. Nevertheless, recent results from molecular and morphometric analyses suggested that this endemic Mediterranean genus comprises four additional species (Wagner et al., 2019) and led to the taxonomic revision of the genus (Wagner et al., 2020). Accordingly, (a) the species name Wagner et al., 2020). ...
... Accordingly, (a) the species name Wagner et al., 2020). Notably, in both the latter regions, the two species are congruent with two morphotypesone slender bodied with a small head and the other stout bodied with a larger headwhich suggests convergent evolution (Wagner et al., 2019). ...
Article
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Otolith morphology is a widely accepted tool for species identification in teleost fish, but whether this holds true for very small species remains to be explored. Here, the saccular otoliths of the cryptobenthic Mediterranean clingfish Gouania (Gobiesocidae) are described for the first time. Our new data, although preliminary, indicate that otolith morphology and morphometry support the recognition of the recently differentiated five species of Gouania in the Mediterranean Sea. Furthermore, otoliths of phylogenetically closely related Gouania species resemble each other more than do those of the more distantly related species. This article is protected by copyright. All rights reserved.
... Interstitial fishes have been considered among the least studied vertebrates (Brandl, Goatley, Bellwood, & Tornabene, 2018;Wagner et al., 2019). Like other interstitial fishes, interstitial trichomycterids are poorly known, with most species described in recent years. ...
... Sand-dwelling trichomycterids are similar to many other psammophilic Neotropical fishes in possessing translucent body and small adult size (Zuanon, Bockmann, & Sazima, 2006). On the other hand, interstitial trichomycterids exhibit uncommon morphology that has convergently occurred in cryptobenthic fishes (Wagner et al., 2019;Yamada, Sugiyama, Tamaki, Kawakita, & Kato, 2009), including elongate eel-shaped body with numerous vertebrae and reduction or absence of eye and fins (Costa & Bockmann, 1994a;de Pinna, 1989a;de Pinna & Kirovsky, 2011;Schaefer, Provenzano, Pinna, & Baskin, 2005). Similar adaptations to interstitial life convergently occurred in so different lineages of marine interstitial teleost fishes such as clingfishes (Wagner et al., 2019) and gobies (Yamada et al., 2009). ...
... On the other hand, interstitial trichomycterids exhibit uncommon morphology that has convergently occurred in cryptobenthic fishes (Wagner et al., 2019;Yamada, Sugiyama, Tamaki, Kawakita, & Kato, 2009), including elongate eel-shaped body with numerous vertebrae and reduction or absence of eye and fins (Costa & Bockmann, 1994a;de Pinna, 1989a;de Pinna & Kirovsky, 2011;Schaefer, Provenzano, Pinna, & Baskin, 2005). Similar adaptations to interstitial life convergently occurred in so different lineages of marine interstitial teleost fishes such as clingfishes (Wagner et al., 2019) and gobies (Yamada et al., 2009). ...
Article
Interstitial trichomycterid catfishes of the Glanapteryginae and Sarcoglanidinae with uncommon morphology have been known for long time from taxa endemic to the Amazon. In most recent decades, two genera, Listrura and Microcambeva, respectively, placed in Glanapteryginae and Sarcoglanidinae on the basis of morphological characters, have been described from the Atlantic Forest of eastern South America, about 1,500 km from the area inhabited by those Amazon taxa. Herein, we first test the phylogenetic positioning of Listrura and Microcambeva using a multigene data set, including two nuclear and three mitochondrial genes for nine species of Listrura and Microcambeva and 11 species representing all closely related subfamilies (TSVSG‐clade), as well as five used as outgroups. The phylogenetic analyses generated a robust tree with high support values in all nodes, where monophyly of Glanapteryginae and Sarcoglanidinae is refuted. In contrast, Listrura and Microcambeva form a highly supported clade, herein formally described as a new subfamily, sister to a clade containing taxa representing the Glanapteryginae, Sarcoglanidinae, Stegophilinae, Tridentinae and Vandelliinae. This study also indicates that Microcambeva and Listrura exhibit divergent evolutionary trends in ecological and morphological attributes. Species of Microcambeva inhabit patches of loose sand and possess morphological traits that were convergently acquired by Amazon sand‐dwelling sarcoglanidines, including loss of body pigmentation and long maxilla. Species of Listrura live burrowed inside small stretches of dense leaf litter and have morphological traits that were convergently acquired by Amazon glanapterygines inhabiting leaf litter bottom rivers, including elongate body, with numerous vertebrae and loss or reduction of all fins.
... In the case of clingfish species, we also checked the hiding places to see if there were nests inside them. We also sampled banks of pebbles in the mediolittoral and upper infralittoral with a bucket and checked for fish with a sieve [36]. After sampling, stones and rocks that were checked for the presence of cryptobenthic fishes were placed in their former position, so that we did not cause damage to the natural habitat. ...
Article
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Cryptobenthic fishes were often overlooked in the past due to their cryptic lifestyle, so knowledge of their ecology is still incomplete. One of the most poorly studied taxa of fishes in the Mediterranean Sea is clingfish. In this paper we examine the habitat preferences of three clingfish species (Lepadogaster lepadogaster, L. candolii, and Apletodon incognitus) occurring in the Gulf of Trieste (Northern Adriatic). The results show that all three species have a cryptic lifestyle and are well-segregated based on their depth distribution and macro- and microhabitat preferences. L. lepadogaster inhabits shallow waters of the lower mediolittoral and upper infralittoral, where it occurs on rocky bottoms under stones. L. candolii similarly occurs in the rocky infralittoral under stones, but below the lower distribution limit of L. lepadogaster, and in seagrass meadows, where it occupies empty seashells. Such hiding places in seagrass meadows are also occupied by A. incognitus, which mostly occurs below the lower distribution limit of L. candolii. Despite the overlap of depth and macrohabitat, the probability of individuals of two species encountering each other or competing in the same habitat is low when the depth range is combined with the microhabitat preferences of these species.
... Research on cryptic diversity has intensified over the last two decades and the existence of cryptic species was demonstrated in various animal groups, as for example in hydrozoans (Holland et al., 2004), arachnids (Crews and Gillespie, 2010;Knee et al., 2012;McHugh et al., 2014;Dziki et al., 2015;Schäffer and Koblmüller, 2020), insects (Hebert et al., 2004;Williams et al., 2006;Zangl et al., 2021), crustaceans (Lee, 2000;Lefébure et al., 2006;Belyaeva and Taylor, 2009), amphibians (Stuart et al., 2006), reptiles (Smith et al., 2011) and fish (Colborn et al., 2001;Wagner et al., 2019). Due to the increasing use of integrative approaches and advanced methods, the number is continuously growing (Knee et al., 2012). ...
Article
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There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.
... The Ovalentaria (Fig. 2) included more than 5000 species and appeared in evolution approximately 91 million years ago (MYA) (Near et al., 2013). They are a species endemic to the Mediterranean Sea (Wagner et al., 2019). ...
Article
Immunoglobulin (Ig) genes encode antibodies in jawed vertebrates. They are essential elements of the adaptive immune response. Ig exists in soluble form or as part of the B cell membrane antigen receptor (BCR). Studies of Ig genes in fish genomes reveal the absence of Ig genes in Gouania willdenowi by deletion of the entire Ig locus from the canonical chromosomal region. The genes coding for integral BCR proteins, CD79a and CD79b, are also absent. Genes exist for T α/β lymphocyte receptors but not for the T γ/δ receptors. The results of the genomic analysis are independently corroborated with RNA-Seq transcriptomes from other Gobiesocidae species. From the transcriptome studies, Ig is also absent from these other Gobiesocidae species, Acyrtus sp. and Tomicodon sp. Present evidence suggests that Ig is missing from all species of the Gobiesocidae family.
... Neither did the Sicily Channel influence the genetic structure of the two studied goby species, unlike is the case of some other fish species, e.g., Dicentrarchus labrax (nDNA microsatellite loci) [97], Sprattus sprattus (mtDNA d-loop) [11], and P. tortonesei (mtDNA 16S, COI) [48], where the Sicily Channel presents an important breakpoint. Although many studies showed a genetic differentiation between populations of the biota of the Adriatic and the Mediterranean Seas, separated by the Otranto strait, e.g., in P. minutus (mtDNA d-loop, cyt b, allozymes) [44][45][46]50], Platichthys flesus (allozymes) [98], Gouania willdenowi (mtDNA COI and 9 nDNA markers) [99] and Sparus aurata (allozymes) [100], neither was the Otranto Strait a biogeographic barrier for G. cruentatus and G. geniporus. ...
Article
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Gobies (Gobiiformes: Gobiidae) are the most species-rich family of fishes in general, and the most abundant fish group in the European seas. Nonetheless, our knowledge on many aspects of their biology, including the population genetic diversity, is poor. Although barriers to gene flow are less apparent in the marine environment, the ocean is not a continuous habitat, as has been shown by studies on population genetics of various marine biota. For the first time, European marine goby species which cannot be collected by common fishery techniques were studied. The population genetic structure of two epibenthic species, Gobius geniporus and Gobius cruentatus, from seven localities across their distribution ranges was assessed, using one mitochondrial (cytochrome b) and one nuclear gene (first intron of ribosomal protein gene S7). Our results showed that there is a great diversity of haplotypes of mitochondrial gene cytochrome b in both species at all localities. Global fixation indices (FST) indicated a great differentiation of populations in both studied gobies. Our results did not show a geographic subdivision to individual populations. Instead, the data correspond with the model of migration which allow divergence and recurrent migration from the ancestral population. The estimated migration routes coincide with the main currents in the studied area. This matches well the biology of the studied species, with adults exhibiting only short-distance movements and planktonic larval stages.
... Assessing the taxonomic diversity in cryptic lineages with little or no ecological and/or morphological divergence is still one of the major challenges in systematic biology (Fišer, Robinson & Malard, 2018), but necessary, as informed estimates on the true diversity of taxa are an important prerequisite for our understanding of their evolutionary significance and role in ecosystems. Recent studies have shown that inconspicuous and/or small taxa, often with a reclusive life style, show particularly high levels of cryptic diversity (Von Saltzwedel, Scheu & Schaefer, 2017;Wagner et al., 2019). Mites are no exception, and indeed, their actual diversity seems to be vastly underestimated, even in common and easily recognizable taxa (Navia et al., 2013;Young et al., 2019;Schäffer, Kerschbaumer & Koblmüller, 2019). ...
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Bark beetles are feared as pests in forestry but they also support a large number of other taxa that exploit the beetles and their galleries. Among arthropods, mites are the largest taxon associated with bark beetles. Many of these mites are phoretic and often involved in complex interactions with the beetles and other organisms. Within the oribatid mite family Scheloribatidae, only two of the three nominal species of Paraleius have been frequently found in galleries of bark beetles and on the beetles themselves. One of the species, P. leontonychus, has a wide distribution range spanning over three ecozones of the world and is believed to be a host generalist, reported from numerous bark beetle and tree species. In the present study, phylogenetic analyses of one mitochondrial and two nuclear genes identified six well supported, fairly divergent clades within P. leontonychus which we consider to represent distinct species based on molecular species delimitation methods and largely congruent clustering in mitochondrial and nuclear gene trees. These species do not tend to be strictly host specific and might occur syntopically. Moreover, mito-nuclear discordance indicates a case of past hybridization/introgression among distinct Paraleius species, the first case of interspecific hybridization reported in mites other than ticks.
... The Adriatic Sea is a biogeographically distinct part of the Mediterranean Sea (Bianchi, 2007;Spalding et al., 2007;examples: Koblmüller, Steinwender, Weiß, & Sefc, 2015;Maltagliati, Di Giuseppe, Barbieri, Castelli, & Dini, 2010;Souche et al., 2015;Wagner et al., 2019), to which it is connected by the narrow Otranto Strait. The 800-km long body of water is enclosed by a regular, sandy and gently sloping coast to the west and a steep, rocky coast along with numerous coastal islands to the east. ...
Article
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Aim Population connectivity of benthic marine organisms depends strongly on planktonic larval dispersal and is controlled by geographic distance and oceanographic structure. We examine isolation by distance versus resistance to barriers (ocean current boundaries) against a background of post‐glacial habitat expansion in a small benthic fish of the Adriatic Sea. Location Adriatic Sea, Eastern Mediterranean. Taxon Tripterygion tripteronotum. Methods We performed population genetic analyses using mitochondrial control region sequences of 550 individuals from 25 locations sampled along the Eastern Adriatic coast. Investigations of population structure included differentiation tests, cluster analyses and distance‐based redundancy analysis. We then ran Lagrangian simulations of passive larval drift to examine correlations among population structure, geographic distance and the Adriatic gyre system. To test for signatures of a post‐glacial range expansion, we modelled the demographic history of the populations and examined the geographic distribution of genetic diversity. Results Genetic population structure corresponded to the Adriatic gyres without additional effect of geographic distance. Inference of northward‐biased gene flow between the northern and the Istrian gyre was consistent with simulated trajectories of passive drift, whereas the phylogeographic break coinciding with the boundary between the Central and the Northern Adriatic gyre was stronger than predicted by drift simulations. Genetic connectivity of populations within gyres was high. Genetic signatures of population expansion were consistent with a rapid post‐glacial recolonization of the northern Adriatic. Main conclusions The combination of dense sampling and passive drift simulation allowed us to distinguish among effects of geographic distance, oceanographic features and palaeoenvironmental changes on current population structure. Comparisons between realized and potential connectivity illustrate the value of integrating different data sources to understand population structure and inform conservation planning.
... It is endemic to the Mediterranean Sea and its distribution ranges from the Eastern to Western Mediterranean. It belongs to the order of the Gobiesociformes (specifically, to the Gobiesocidae family), being the only representative of its genus, however recently five species have been described using morphometric studies and analysis of different genes (Wagner et al., 2019). ...
Preprint
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In the study of immunoglobulin V genes in fish genomes, we found that the species Gouania willdenowi does not possess any such regions, neither for the heavy chain nor for the light chains. Also, genes that code for the immunoglobulin constant regions were also not found. A detailed analysis of the chromosomal region of these genes revealed a deletion in the entire locus for regions of the heavy and light chains. These studies provide evidence that this species does not possess genes coding for immunoglobulins. Additionally, we found the genes that code for CD79a and CD79b protein molecules have also been deleted. Regions for the Tα/β lymphocyte receptors are present but the T γ/δ receptors were not found. In transcripts of two other Gobiesocidae species, Acystus sp. and Tomicodon sp., no antibody sequences could be detected, possibly indicating the absence of immunoglobulins in all species of this family.
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The Microcambevinae are a catfish subfamily endemic to the Brazilian Atlantic Forest, comprising rare species with interstitial habits. Microcambevines have been classified in two genera, Listrura and Microcambeva, but the relationships among included intrageneric lineages are still poorly understood. The objectives of this study are to conduct a phylogenetic analysis integrating morphological characters and a multigene dataset, and to propose a classification better reflecting morphological diversity and phylogenetic relationships. Phylogenetic analyses combining 57 morphological characters and a 2563 bp molecular dataset generated similar phylogenetic trees with high support values for most clades, including the two genera and some intrageneric groups. Six morphologically distinctive infrageneric lineages, three in Listrura and three in Microcambeva, are classified as subgenera, as well as two new species are described. The morphological diversity here recorded integrated to available information about habitat indicate high level of divergent specialisation among lineages. The analyses indicate a series of convergent morphological traits between Listrura and other teleosts sharing a fossorial lifestyle, as well as specialised traits independently occurring within Listrura lineages. Similarly, a great diversity of morphological traits occurs convergently in Microcambeva lineages and other teleosts sharing psammophilic habits. This study shows that combining molecular and morphological data yields well-supported phylogenies, making possible to unambiguously diagnose clades and to establish evolutionary hypothesis on morphological evolution.
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We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available. The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Alexandros.Stamatakis@h-its.org.
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Spatial priorities for the conservation of three key Mediterranean habitats, i.e. seagrass Posidonia oceanica meadows, coralligenous formations, and marine caves, were determined through a systematic planning approach. Available information on the distribution of these habitats across the entire Mediterranean Sea was compiled to produce basin-scale distribution maps. Conservation targets for each habitat type were set according to European Union guidelines. Surrogates were used to estimate the spatial variation of opportunity cost for commercial, non-commercial fishing, and aquaculture. Marxan conservation planning software was used to evaluate the comparative utility of two planning scenarios: (a) a whole-basin scenario, referring to selection of priority areas across the whole Mediterranean Sea, and (b) an ecoregional scenario, in which priority areas were selected within eight predefined ecoregions. Although both scenarios required approximately the same total area to be protected in order to achieve conservation targets, the opportunity cost differed between them. The whole-basin scenario yielded a lower opportunity cost, but the Alboran Sea ecoregion was not represented and priority areas were predominantly located in the Ionian, Aegean, and Adriatic Seas. In comparison, the ecoregional scenario resulted in a higher representation of ecoregions and a more even distribution of priority areas, albeit with a higher opportunity cost. We suggest that planning at the ecoregional level ensures better representativeness of the selected conservation features and adequate protection of species, functional, and genetic diversity across the basin. While there are several initiatives that identify priority areas in the Mediterranean Sea, our approach is novel as it combines three issues: (a) it is based on the distribution of habitats and not species, which was rarely the case in previous efforts, (b) it considers spatial variability of cost throughout this socioeconomically heterogeneous basin, and (c) it adopts ecoregions as the most appropriate level for large-scale planning.
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The Messinian salinity crisis is widely regarded as one of the most dramatic episodes of oceanic change of the past 20 or so million years (refs 1-3). Earliest explanations were that extremely thick evaporites were deposited in a deep and desiccated Mediterranean basin that had been repeatedly isolated from the Atlantic Ocean, but elucidation of the causes of the isolation - whether driven largely by glacio-eustatic or tectonic processes - have been hampered by the absence of an accurate time frame. Here we present an astronomically calibrated chronology for the Mediterranean Messinian age based on an integrated high-resolution stratigraphy and 'tuning' of sedimentary cycle patterns to variations in the Earth's orbital parameters. We show that the onset of the Messinian salinity crisis is synchronous over the entire Mediterranean basin, dated at 5.96 ± 0.02 million years ago. Isolation from the Atlantic Ocean was established between 5.59 and 5.33 million years ago, causing a large fall in Mediterranean water level followed by erosion (5.59-5.50 million years ago) and deposition (5.50- 5.33 million years ago) of non-marine sediments in a large 'Lago Mare' (Lake Sea) basin. Cyclic evaporite deposition is almost entirely related to circum- Mediterranean climate changes driven by changes in the Earth's precession, and not to obliquity-induced glacio-eustatic sea-level changes. We argue in favour of a dominantly tectonic origin for the Messinian salinity crisis, although its exact timing may well have been controlled by the ~400-kyr component of the Earth's eccentricity cycle.
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Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the "bush at the top" of the teleost tree, and indicates acanthomorphs originated in the Early Cretaceous. Paleontological evidence suggests acanthomorphs exhibit a pulse of morphological diversification following the end Cretaceous mass extinction; however, the role of this event on the accumulation of living acanthomorph diversity remains unclear. Lineage diversification rates through time exhibit no shifts associated with the end Cretaceous mass extinction, but there is a global decrease in lineage diversification rates 50 Ma that occurs during a period when morphological disparity among fossil acanthomorphs increases sharply. Analysis of clade-specific shifts in diversification rates reveal that the hyperdiversity of living acanthomorphs is highlighted by several rapidly radiating lineages including tunas, gobies, blennies, snailfishes, and Afro-American cichlids. These lineages with high diversification rates are not associated with a single habitat type, such as coral reefs, indicating there is no single explanation for the success of acanthomorphs, as exceptional bouts of diversification have occurred across a wide array of marine and freshwater habitats.
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Superimposition methods for comparing configurations of landmarks in two or more specimens are reviewed. These methods show differences in shape among specimens as residuals after rotation, translation, and scaling them so that they align as well as possible. A new method is presented that generalizes Siegel and Benson's (1982) resistant-fit theta-rho analysis so that more than two objects can be compared at the same time. Both least-squares and resistant-fit approaches are generalized to allow for affine transformations (uniform shape change). The methods are compared, using artificial data and data on 18 landmarks on the wings of 127 species of North American mosquitoes. Graphical techniques are also presented to help summarize the patterns of differences in shape among the objects being compared.
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Molecular methods are increasingly being used in the study of harmful microalgae; however, DNA extraction techniques have imposed limitations on the species and questions studied, with research primarily restricted to cultured specimens. Here we describe a simple method that merges two existing techniques for DNA extraction from live and preserved single dinoflagellate cells. DNA was successfully isolated from live single cells of Gambierdiscus toxicus Adachi et Fukuyo, 1979 and cells preserved using formalin/methanol fixation. This method supplements existing techniques and expands the scope of genetics studies conducted on dinoflagellates to include routine molecular analysis of single cells isolated from field samples.
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Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With technological advances, it is now becoming more common to collect data sets containing multiple gene loci and multiple individuals per species. These data sets often reveal the need to directly model intraspecies polymorphism and incomplete lineage sorting in phylogenetic estimation procedures. For a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. Here, we present a Bayesian Markov chain Monte Carlo method for the multispecies coalescent. Our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. The inference is made possible by multilocus data from multiple individuals per species. Using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. These simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. Finally, we compare our new method to both an existing method (BEST 2.2) with similar goals and the supermatrix (concatenation) method. We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation.
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The seacoasts of the Japanese Arc are fringed by many gravel beaches owing to active tectonic uplift and intense denudation caused by heavy rainfall. These gravel beaches are inhabited by gobies of the genus Luciogobius that burrow into the gravel sediment and live interstitially. Although their habitat and morphology (e. g., reduced fins, elongated, scale-less body, and highly segmented vertebral column) are highly unusual among fishes, little is known on how their morphological evolution has facilitated the colonization of interstitial habitats and promoted extensive diversification. We conducted thorough sampling of Luciogobius and related species throughout Japan, and performed molecular phylogenetic analysis to explore the patterns of morphological evolution associated with gravel beach colonization. An analysis of the mitochondrial cytochrome b gene suggested a remarkable diversity of previously unrecognized species. The species-level phylogeny based on six protein-coding nuclear genes clearly indicated that interstitial species cluster into two distinct clades, and that transitions from benthic or demersal habits to interstitial habits are strongly correlated with an increase in vertebral number. Colonization of gravel beach habitats is estimated to have occurred ca. 10 Ma, which coincides with the period of active orogenesis of the Japanese landmass. Different species of interstitial Luciogobius inhabit sediments with different granulometric properties, suggesting that microhabitat partitioning has been an important mechanism facilitating speciation in these fishes. This is the first study to document the adaptation to interstitial habitats by a vertebrate. Body elongation and excessive vertebral segmentation had been the key aspects enhancing body flexibility and fishes' ability to burrow into the gravel sediment. The rich diversity of coastal gravel habitats of the Japanese Arc has likely promoted the adaptive radiation of these unique gravel-dwelling fishes.
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The spatial distribution of neutral genetic diversity is mainly influenced by barriers to dispersal. The nature of such barriers varies according to the dispersal means and capabilities of the organisms concerned. Although these barriers are often obvious on land, in the ocean they can be more difficult to identify. Determining the relative influence of physical and biotic factors on genetic connectivity remains a major challenge for marine ecologists. Here, we compare gene flow patterns of 7 littoral fish species from 6 families with a range of early-life-history traits sampled at the same geographic locations across common environmental discontinuities in the form of oceanic fronts in the Western Mediterranean. We show that these fronts represent major barriers to gene flow and have a strong influence on the population genetic structure of some fish species. We also found no significant relation between the early-life-history traits most commonly investigated (egg type, pelagic larval duration, and inshore-offshore spawning) and gene flow patterns, suggesting that other life-history factors should deserve attention. The fronts analyzed and the underlying physical mechanisms are not site-specific but common among the oceans, suggesting the generality of our findings.
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Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.
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Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new phylogenetic makers. We report here a genome-comparison strategy to identifying nuclear gene markers for phylogenetic inference and apply it to the ray-finned fishes--the largest vertebrate clade in need of phylogenetic resolution. A total of 154 candidate molecular markers--relatively well conserved, putatively single-copy gene fragments with long, uninterrupted exons--were obtained by comparing whole genome sequences of two model organisms, Danio rerio and Takifugu rubripes. Experimental tests of 15 of these (randomly picked) markers on 36 taxa (representing two-thirds of the ray-finned fish orders) demonstrate the feasibility of amplifying by PCR and directly sequencing most of these candidates from whole genomic DNA in a vast diversity of fish species. Preliminary phylogenetic analyses of sequence data obtained for 14 taxa and 10 markers (total of 7,872 bp for each species) are encouraging, suggesting that the markers obtained will make significant contributions to future fish phylogenetic studies. We present a practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny. Our method is an improvement over traditional approaches (e.g., manually picking genes for testing) because it uses genomic information and automates the process to identify large numbers of candidate makers. This approach is shown here to be successful for fishes, but also could be applied to other groups of organisms for which two or more complete genome sequences exist, which has important implications for assembling the tree of life.
Book
Available online under http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp
Book
Statistics of numbers of nominal and valid species described in families and subfamilies of recent fishes. Available under http://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp
Article
Astronomical tuning of the Messinian pre-salt succession in the Levant Basin allows for the first time the reconstruction of a detailed chronology of the Messinian salinity crisis (MSC) events in deep setting and their correlation with marginal records that supports the CIESM (2008) 3-stages model. Our main conclusions are: i)MSC events were synchronous across marginal and deep basins; i)MSC onset in deep basins occurred at 5.97 Ma; ii)only foraminifera-barren, evaporite-free shales accumulated in deep settings between 5.97 and 5.60 Ma; iii)deep evaporites (anhydrite and halite) deposition started later, at 5.60 Ma; iv)new and published 87Sr/86Sr data, indicate that during all stages, evaporites precipitated from the same water-body in all the Mediterranean sub-basins; The wide synchrony of events and 87Sr/86Sr homogeneity implies inter-sub-basin connection during the whole MSC and is not compatible with large sea-level fall and desiccation of the Mediterranean. This article is protected by copyright. All rights reserved.
Article
Percomorph fishes are relatively uncommon in the Sarmatian deposits of Dolje and Belgrade where they are primarily of small size, often representing juvenile specimens. Here, we describe otoliths in situ from “Scorpaena” minima Kramberger 1882 (Scorpaenidae), Symphodus woodwardi (Kramberger 1891) (Labridae), and from an indeterminate clingfish tentatively placed in Apletodon (Gobiesocidae). “Scorpaena” minima is based on juvenile specimens and does not exhibit a complete set of features for a robust diagnosis, although it certainly represents a nominally valid species. Symphodus woodwardi is redefined herein based on the holotype and an additional small and well-preserved specimen, and a comparative analysis including Neogene congeners from the Mediterranean and Paratethys is discussed. Apletodon? sp. represents the first documented fossil clingfish in the record, even if the preservation of the three specimens identified does not allow a detailed taxonomic definition to the species level. None of the species with otolith in situ described herein can be related to any of the known coeval isolated otolith-based species, although in the case of the scorpaenid, such correlation is hampered by the juvenile nature of the available specimens.
Article
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
Article
Increasingly, data on shape are analysed in combination with molecular genetic or ecological information, so that tools for geometric morphometric analysis are required. Morphometric studies most often use the arrangements of morphological landmarks as the data source and extract shape information from them by Procrustes superimposition. The MorphoJ software combines this approach with a wide range of methods for shape analysis in different biological contexts. The program offers an integrated and user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. MorphoJ is written in Java and versions for the Windows, Macintosh and Unix/Linux platforms are freely available from http://www.flywings.org.uk/MorphoJ_page.htm.
Article
Dispersal of planktonic larvae can create connections between geographically separated adult populations of benthic marine animals. How geographic context and life history traits affect these connections is largely unresolved. We use data from genetic studies (species level FST) of benthic teleost fishes combined with linear models to evaluate the importance of transitions between biogeographic regions, geographic distance, egg type (benthic or pelagic eggs), pelagic larval duration (PLD), and type of genetic marker as factors affecting differentiation within species. We find that transitions between biogeographic regions and egg type are significant and consistent contributors to population genetic structure, whereas PLD does not significantly explain population structure. Total study distance frequently contributes to significant interaction terms, particularly in association with genetic markers, whereby FST increases with study distance for studies employing mtDNA sequences, but allozyme and microsatellite studies show no increase in FST with study distance. These results highlight the importance of spatial context (biogeography and geographic distance) in affecting genetic differentiation and imply that there are inherent differences in dispersal ability associated with egg type. We also find that the geographic distance over which the maximum pairwise FST between populations occurs (relative to total study distance) is highly variable and can be observed at any scale. This result is consistent with stochastic processes inflating genetic differentiation and/or insufficient consideration of geographic and biological factors relevant to connectivity.
Article
This study addresses the habitat and microhabitat of the seven species of gobiesocid fish in the Mediterranean Sea. It is shown that Lepadogaster lepadogaster is closely adapted to large pebbles and boulder fields of rounded stones with a smooth surface. L. candollei is more euryecious and, in addition to inhabiting boulder fields also, occurs close to seagrass meadows, in small cavities and in association with sea urchins. Diplecogaster bimaculata is also euryecious and extends to greater depths. It lives on sand and muddy bottoms as well as on coralline grounds. At some locations this species is found in high abundance during the spawning season under empty bivalve shells or flat stones. Apletodon dentatus is the rarest species of Gobiesocidae in the Mediterranean Sea. It has a close association with seagrass or large brown algae (Cystoseira). Juveniles of A. incognitus are either associated with sea urchins or inhabit Posidonia meadows. Adults prefer the vicinity of seagrass meadows under empty bivalve shells and stones overgrown with red algae. Gouania wildenowi is stenoecious and is restricted to the interstices of roundish coarse gravel near the waterline. Opeatogenys gracilis is also stenoecious and lives only on the leaves of Posidonia and Cymodocea seagrass. The colourations of the different species and their variations are described and discussed.
Article
Genetic connectivity and geographic fragmentation are two opposing mechanisms determining the population structure of species. While the first homogenizes the genetic background across populations the second one allows their differentiation. Therefore, knowledge of processes affecting dispersal of marine organisms is crucial to understand their genetic distribution patterns and for the effective management of their populations. In this study, we use genetic analyses of eleven microsatellites in combination with oceanographic satellite and dispersal simulation data to determine distribution patterns for Serranus cabrilla, a ubiquitous demersal broadcast spawner, in the Mediterranean Sea. Pairwise population F(ST) values ranged between -0.003 and 0.135. Two genetically distinct clusters were identified, with a clear division located between the oceanographic discontinuities at the Ibiza Channel (IC) and the Almeria-Oran Front (AOF), revealing an admixed population in between. The Balearic Front (BF) also appeared to dictate population structure. Directional gene flow on the Spanish coast was observed as S. cabrilla dispersed from west to east over the AOF, from north to south on the IC and from south of the IC towards the Balearic Islands. Correlations between genetic and oceanographic data were highly significant. Seasonal changes in current patterns and the relationship between ocean circulation patterns and spawning season may also play an important role in population structure around oceanographic fronts.
Article
The conditions of phenotypic and genetic population differentiation allow inferences about the evolution, preservation and loss of biological diversity. In Lake Tanganyika, water level fluctuations are assumed to have had a major impact on the evolution of stenotopic littoral species, though this hypothesis has not been specifically examined so far. The present study investigates whether subtly differentiated colour patterns of adjacent Tropheus moorii populations are maintained in isolation or in the face of continuous gene flow, and whether the presumed influence of water level fluctuations on lacustrine cichlids can be demonstrated in the small-scale population structure of the strictly stenotopic, littoral Tropheus. Distinct population differentiation was found even across short geographic distances and minor habitat barriers. Population splitting chronology and demographic histories comply with our expectation of old and rather stable populations on steeper sloping shore, and more recently established populations in a shallower region. Moreover, population expansions seem to coincide with lake level rises in the wake of Late Pleistocene megadroughts ~100 KYA. The imprint of hydrologic events on current population structure in the absence of ongoing gene flow suggests that phenotypic differentiation among proximate Tropheus populations evolves and persists in genetic isolation. Sporadic gene flow is effected by lake level fluctuations following climate changes and controlled by the persistence of habitat barriers during lake level changes. Since similar demographic patterns were previously reported for Lake Malawi cichlids, our data furthermore strengthen the hypothesis that major climatic events synchronized facets of cichlid evolution across the East African Great Lakes.
Article
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log‐expectation score, and refinement using tree‐dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T‐Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T‐Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
Article
Several characteristics of the Gobiesocidae, such as the fact that they are small cryptic fishes, could explain the scarcity of studies on these species when compared with other rocky littoral fish families. Analyses of molecular and meristic data are in agreement with the views of previous workers. The genus Lepadogaster must be redefined to include only the species L. lepadogaster (Bonaterre, 1788) and L. purpurea (Bonaterre, 1788). For the time being the genus Mirbelia should be revalidated and redefined to include only the species Mirbelia candollei (Risso, 1810). This proposal has the advantage of calling attention to the need to separate M. candollei from Lepadogaster and to its distinctiveness from other clingfishes.
DensiTree 2: Seeing trees through the forest
  • Bouckaert
Bouckaert, R., Heled, J., 2014. DensiTree 2: Seeing trees through the forest. bioRxiv -Prepr. Serv. 1-11.
Taxonomie, Verbreitung und Ökologie von Schildfischen der Unterfamilie Lepadogastrinae (Gobiesocidae, Teleostei)
  • R Hofrichter
Hofrichter, R., 1995. Taxonomie, Verbreitung und Ökologie von Schildfischen der Unterfamilie Lepadogastrinae (Gobiesocidae, Teleostei). Unpublished doctoral thesis (Naturwissenschaftliche Fakultät, Paris Lodron Universität Salzburg), viii + 448 pp.
Meeresfische: Westeuropa und Mittelmeer
  • P Louisy
Louisy, P., 2002. Meeresfische: Westeuropa und Mittelmeer. Verlag Eugen Ulmer, Stuttgart.