@article{KetmaierMandatoriDeMatthaeisetal.2005,
  author    = {Ketmaier, Valerio and Mandatori, R. and De Matthaeis, E. and Mura, G.},
  title     = {Molecular systematics and phylogeography in the fairy shrimp Tanymastix stagnalis based on mitochondrial DNA},
  issn      = {0952-8369},
  year      = {2005},
  abstract  = {Patterns of sequence divergence in about 1 kb of mitochondrial DNA coding for two genes (16s rRNA and cytochrome oxidase I, COI) were analysed in 13 populations of the fairy shrimp Tanymastix stagnalis from Norway, Germany, France, Italy (northern and central Italy plus insular populations from Sardinia and the Tuscan Archipelago) and Spain, and in one presumed population of Tanymastix stellae from Corsica. The latter species was originally known only from a single locality in Sardinia, which has been destroyed by urbanization; the Corsican population was referred to T stellae by some French authors on the basis of the collection of several cysts from mud. mtDNA data revealed a very low level of genetic divergence between the presumed population of T stellae and the other T stagnalis populations included in the study. Our genetic findings do not support the presence of T stellae in Corsica and are in line with previous SEM studies revealing that all species belonging to the genus Tanymastix produce cysts with identical morphology. The results indicate complex phylogeographic relationships and pronounced genetic differentiation among T stagnalis populations. The islands of Corsica and Sardinia on the one hand and the island of Capraia (Tuscan Archipelago) on the other were probably colonized independently at different times. Genetic relationships among continental populations do not follow a clear geographical trend, indicating that geographical distance is not the main force shaping the pattern of genetic structuring of the species. Stochastic factors such as multiple and independent founder events probably contributed to the striking pattern of genetic differentiation along with subsequent local adaptation. These results agree with previously published molecular work on several groups of aquatic organisms and further support the high potential for dispersal-low gene flow paradox shown by a large array of animals living in lentic habitats},
  language  = {en}
}
@article{KetmaierBernardini2005,
  author    = {Ketmaier, Valerio and Bernardini, C.},
  title     = {Structure of the mitochondrial control region of the Eurasian otter (Lutra lutra ; Carnivora, Mustelidae): patterns of genetic heterogeneity and implications for conservation of the species in Italy},
  issn      = {0022-1503},
  year      = {2005},
  abstract  = {In this study we determined the complete sequence of the mitochondrial DNA (mtDNA) control region of the Eurasian otter (Lutra lutra). We then compared these new sequences with orthologues of nine carnivores belonging to six families (Mustelidae, Mephitidae, Canidae, Hyaenidae, Ursidae, and Felidae). The comparative analyses identified all the conserved regions previously found in mammals. The Eurasian otter and seven other species have a single location with tandem repeats in the right domain, while the spotted hyena (Hyaenidae) and the tiger (Felidae) have repeated sequences in both the right and left domains. To assess the degree of genetic heterogeneity of the Eurasian otter in Italy we sequenced two fragments of the gene and analyzed length polymorphisms of repeated sequences and heteroplasmy in 32 specimens. The study includes 23 museum specimens collected in northern, central, and southern Italy; most of these specimens are from extinct populations, while the southern Italian samples belong to the sole extant Italian population of the Eurasian otter. The study also includes all the captive-reared animals living in the colony "Centro Lontra, Caramanico Terme" (Pescara, central Italy). The colony is maintained for reintroduction of the species. We found a low level of genetic polymorphism; a single haplotype is dominant, but our data indicate the presence in central and southern Italy of two slightly divergent haplotypes. One haplotype belongs to an extinct population, the other is present in the single extant Italian population. Analyses of length polymorphisms and heteroplasmy indicate that the autochthonous Italian samples are characterized by a distinct array of repeated sequences from captive-reared animals},
  language  = {en}
}
@article{FeulnerKirschbaumSchugardtetal.2006,
  author    = {Feulner, Philine G. D. and Kirschbaum, Frank and Schugardt, Christian and Ketmaier, Valerio and Tiedemann, Ralph},
  title     = {Electrophysiological and molecular genetic evidence for sympatrically occuring cryptic species in African weakly electric fishes (Teleostei : Mormyridae : Campylomormyrus)},
  issn      = {1055-7903},
  doi       = {10.1016/j.ympev.2005.09.008},
  year      = {2006},
  abstract  = {For two sympatric species of African weakly electric fish, Campylomormyrus tamandua and Campylomormyrus numenius, we monitored ontogenetic differentiation in electric organ discharge (EOD) and established a molecular phylogeny, based on 2222 bp from cytochrome b, the S7 ribosomal protein gene, and four flanking regions of unlinked microsatellite loci. In C tamandua, there is one common EOD type, regardless of age and sex, whereas in C numenius we were able to identify three different male adult EOD waveform types, which emerged from a single common EOD observed in juveniles. Two of these EOD types formed well supported clades in our phylogenetic analysis. In an independent line of evidence, we were able to affirm the classification into three groups by microsatellite data. The correct assignment and the high pairwise FST values support our hypothesis that these groups are reproductively isolated. We propose that in C numenius there are cryptic species, hidden behind similar and, at least as juveniles, identical morphs.},
  language  = {en}
}
@article{BiancoZupoKetmaier2006,
  author    = {Bianco, Pier Giorgio and Zupo, V and Ketmaier, Valerio},
  title     = {Occurrence of the scalloped ribbonfish Zu cristatus(Lampridiformes) in coastal waters of the central Tyrrhenian Sea, Italy},
  issn      = {0022-1112},
  doi       = {10.1111/j.1095-8649.2006.00980.x},
  year      = {2006},
  abstract  = {The occurrence of two individuals of Zu cristatus at 2 m depth in coastal waters of the Gulf of Castellamare (Tyrrhenian Sea, Italy) together with records of this rare pan-Oceanic mesopelagic species is reported. Analyses of two mitochondrial genes (12 s and 16 s; 936 bp) revealed a 2.6\% sequence divergence between Mediterranean and Pacific (Japanese) samples of the species.},
  language  = {en}
}
@article{KetmaierGiustiCaccone2006,
  author    = {Ketmaier, Valerio and Giusti, Folco and Caccone, Adalgisa},
  title     = {Molecular phylogeny and historical biogeography of the land snail genus Solatopupa (Pulmonata) in the peri- Tyrrhenian area},
  issn      = {1055-7903},
  doi       = {10.1016/j.ympev.2005.12.008},
  year      = {2006},
  abstract  = {The land snail genus Solatopupa consists of six species and has a peri-Tyrrhenian distribution; most of the species have a very narrow range and all of them except one (Solatopupa cianensis, which inhabits porphyritic rocks) are strictly bound to calcareous substrates. One species (Solatopupa gidoni) is limited to Sardinia, Corsica, and Elba Island. Because the potential for dispersal of these snails is low, the insular range of this species has been traditionally related to the Oligocenic detachment of the Sardinia-Corsica microplate from the Iberian plate and its subsequent rotation towards the Italian peninsula. In this Study, we used sequences of three mitochondrial and one nuclear gene to reconstruct the evolutionary history of the genus. Our phylogenetic results are consistent with the genetic relationships found using allozymes, but contrast with the phylogenetic hypotheses based on karyology and morphology. Molecular clock estimates indicate that the main cladogenetic events in the genus occurred between the middle Miocene and the middle-late Pliocene. Patterns of phylogenetic relationships and geological considerations suggest that the cladogenesis of the genus can be explained by vicariant (tectonic) processes. Our datings do not support a causal relation between the split of S. guidoni from its continental sister taxon and the initial phases of the detachment of the Corsica-Sardinia microplate from the mainland. On the contrary, time estimates coincide with the very last phase of detachment of the microplate (from 5 to 3 Myrs ago). Overall, our molecular clock estimates are in good agreement with the latest geological views on the tectonic evolution of the peri-Tyrrhenian area.},
  language  = {en}
}
@article{KetmaierFinamoreLargiaderetal.2009,
  author    = {Ketmaier, Valerio and Finamore, Francesco and Largiader, Carlo Rodolfo and Milone, Marco and Bianco, Pier Giorgio},
  title     = {Phylogeography of bleaks Alburnus spp. (Cyprinidae) in Italy, based on cytochrome b data},
  issn      = {0022-1112},
  doi       = {10.1111/j.1095-8649.2009.02357.x},
  year      = {2009},
  abstract  = {Sequence variation of a fragment of the mitochondrial DNA encoding for the cytochrome b gene was used to reconstruct the phylogeography of the two species of bleaks occurring in Italy: the alborella Alburnus arborella in northern Italy and the vulturino Alburnus albidus in southern Italy. The study includes four populations of the alborella and 14 populations of the vulturino. A total of 57 haplotypes were identified; these could not be sorted into two reciprocally monophyletic clusters. Multiple phylogenetic methods and nested clade phylogeographical analysis consistently retrieved three well-supported clades, two of which contained both Northern and Southern Italian haplotypes. A third clade is limited to southern Italy. This clade is tentatively assigned to the vulturino. The placement in the same clade of northern and southern Italian haplotypes is explained in light of the introductions of fishes operated from northern to central and southern Italy. The origin of the vulturino dates back to the last two million years. This divergence time estimate identifies the Pleistocene confluences between adjacent river basins along the Adriatic slope of the Italian peninsula and their subsequent isolation as the cause that triggered the diversification of the genus in the area. The existence of a clade endemic to southern Italy supports the recognition of the area as a new peri-Mediterranean ichthyogeographic district, the borders of which correspond to the northern and southern edges of the vulturino range.},
  language  = {en}
}
@article{SalaBozanoKetmaierMariani2009,
  author    = {Sala-Bozano, Maria and Ketmaier, Valerio and Mariani, Stefano},
  title     = {Contrasting signals from multiple markers illuminate population connectivity in a marine fish},
  issn      = {0962-1083},
  doi       = {10.1111/j.1365-294X.2009.04404.x},
  year      = {2009},
  abstract  = {Recent advances in molecular biology and bioinformatics have helped to unveil striking and previously unrecognized patterns of geographic genetic structure in marine populations. Largely driven by the pressing needs of fisheries management and conservation, studies on marine fish populations have played a pivotal role in testing the efficiency of a range of approaches to explore connectivity and dispersal at sea. Here, we employed nuclear and mitochondrial DNA markers and parasitic infestations to examine the nature and patterns of population structure in a warm-temperate coastal marine teleost across major putative biogeographic barriers in the Mediterranean Sea and Eastern Atlantic Ocean. We detected deep genetic divergence between mitochondrial lineages, likely caused by dramatic climatic and geological transformations before and during the Pleistocene. Such long-diverged lineages later came into secondary contact and can now be found in sympatry. More importantly, microsatellite data revealed that these lineages, after millions of years of independent evolution, now interbreed extensively. By combining genetic and parasite data, we were able to identify at least five independent demographic units. While the different genetic and parasite-based methods produce notably contrasting signals and may complicate the reconstruction of connectivity dynamics, we show that by tailoring the correct interpretation to each of the descriptors used, it is possible to achieve a deeper understanding of the micro-evolutionary process and, consequently, resolve population structure.},
  language  = {en}
}
@article{ApioKabasaKetmaieretal.2010,
  author    = {Apio, Ann and Kabasa, John David and Ketmaier, Valerio and Schroeder, Christoph and Plath, Martin and Tiedemann, Ralph},
  title     = {Female philopatry and male dispersal in a cryptic, bush-dwelling antelope : a combined molecular and behavioural approach},
  issn      = {0952-8369},
  doi       = {10.1111/j.1469-7998.2009.00654.x},
  year      = {2010},
  abstract  = {In most mammals, females are philopatric while males disperse in order to avoid inbreeding. We investigated social structure in a solitary ungulate, the bushbuck Tragelaphus sylvaticus in Queen Elizabeth National Park, Uganda by combining behavioural and molecular data. We correlated spatial and social vicinity of individual females with a relatedness score obtained from mitochondrial DNA analysis. Presumed clan members shared the same haplotype, showed more socio-positive interactions and had a common home range. Males had a higher haplotype diversity than females. All this suggests the presence of a matrilineal structure in the study population. Moreover, we tested natal dispersal distances between male and female yearlings and used control region sequences to confirm that females remain in their natal breeding areas whereas males disperse. In microsatellite analysis, males showed a higher genetic variability than females. The impoverished genetic variability of females at both molecular marker sets is consistent with a philopatric and matrilineal structure, while the higher degree of genetic variability of males is congruent with a higher dispersal rate expected in this sex. Evidence even for male long-distance dispersal is brought about by one male carrying a haplotype of a different subspecies, previously not described to occur in this area.},
  language  = {en}
}
@article{SilvaIturrizaKetmaierTiedemann2010,
  author    = {Silva-Iturriza, Adriana and Ketmaier, Valerio and Tiedemann, Ralph},
  title     = {Mitochondrial DNA suggests multiple colonizations of central Philippine islands (Boracay, Negros) by the sedentary Philippine bulbul Hypsipetes philippinus guimarasensis (Aves)},
  issn      = {0947-5745},
  doi       = {10.1111/j.1439-0469.2010.00566.x},
  year      = {2010},
  abstract  = {In this study, we have used fragments of three mitochondrial genes (Control Region, CR; transfer RNA for methionine, tRNA-Met; NADH dehydrogenase subunit 2, ND2 for a total of 1066 bp) to reconstruct the phylogeographic history of the endemic Philippine bulbul (Hypsipetes philippinus) at the scale of the central area of the Philippine archipelago. The study includes two of the five recognized subspecies (guimarasensis and mindorensis), 7 populations and 58 individuals. Multiple phylogenetic and network analyses support the existence of two reciprocally monophyletic maternal lineages corresponding to the two named subspecies. Molecular clock estimates indicate that the split between the two subspecies is consistent with the Pleistocene geological history of the archipelago. Patterns of relationships within guimarasensis are biogeographically less clear. Here, a combination of vicariance and dispersal needs to be invoked to reconcile the molecular data with the geographical origin of samples. In particular, the two islands Boracay and Negros host mitochondrial lineages that do not form monophyletic clusters. Our genetic data suggest multiple independent colonization events for these locations.},
  language  = {en}
}
@article{WiemannAndersenBerggrenetal.2010,
  author    = {Wiemann, Annika and Andersen, Liselotte W. and Berggren, Per and Siebert, Ursula and Benke, Harald and Teilmann, Jonay and Lockyer, Christina and Pawliczka, Iwona and Skora, Krysztof and Roos, Aanna and Lyrholm, Thomas and Paulus, Kirsten B. and Ketmaier, Valerio},
  title     = {Mitochondrial Control Region and microsatellite analyses on harbour porpoise (Phocoena phocoena) unravel population differentiation in the Baltic Sea and adjacent waters},
  issn      = {1566-0621},
  doi       = {10.1007/s10592-009-0023-x},
  year      = {2010},
  abstract  = {The population status of the harbour porpoise (Phocoena phocoena) in the Baltic area has been a continuous matter of debate. Here we present the by far most comprehensive genetic population structure assessment to date for this region, both with regard to geographic coverage and sample size: 497 porpoise samples from North Sea, Skagerrak, Kattegat, Belt Sea, and Inner Baltic Sea were sequenced at the mitochondrial Control Region and 305 of these specimens were typed at 15 polymorphic microsatellite loci. Samples were stratified according to sample type (stranding vs. by- caught), sex, and season (breeding vs. non-breeding season). Our data provide ample evidence for a population split between the Skagerrak and the Belt Sea, with a transition zone in the Kattegat area. Among other measures, this was particularly visible in significant frequency shifts of the most abundant mitochondrial haplotypes. A particular haplotype almost absent in the North Sea was the most abundant in Belt Sea and Inner Baltic Sea. Microsatellites yielded a similar pattern (i.e., turnover in occurrence of clusters identified by STRUCTURE). Moreover, a highly significant association between microsatellite assignment and unlinked mitochondrial haplotypes further indicates a split between North Sea and Baltic porpoises. For the Inner Baltic Sea, we consistently recovered a small, but significant separation from the Belt Sea population. Despite recent arguments that separation should exceed a predefined threshold before populations shall be managed separately, we argue in favour of precautionary acknowledging the Inner Baltic porpoises as a separate management unit, which should receive particular attention, as it is threatened by various factors, in particular local fishery measures.},
  language  = {en}
}
@article{PavesiDeMatthaeisTiedemannetal.2011,
  author    = {Pavesi, Laura and De Matthaeis, Elvira and Tiedemann, Ralph and Ketmaier, Valerio},
  title     = {Temporal population genetics and COI phylogeography of the sandhopper macarorchestia remyi (Amphipoda: Talitridae)},
  series = {Zoological studies},
  volume    = {50},
  journal   = {Zoological studies},
  number    = {2},
  publisher = {Institute of Zoology, Academia Sinica},
  address   = {Taipei},
  issn      = {1021-5506},
  pages     = {220 -- 229},
  year      = {2011},
  abstract  = {Laura Pavesi, Elvira De Matthaeis, Ralph Tiedemann, and Valerio Ketmaier (2011) Temporal population genetics and COI phylogeography of the sandhopper Macarorchestia remyi (Amphipoda: Talitridae). Zoological Studies 50(2): 220-229. In this study we assessed levels of genetic divergence and variability in 208 individuals of the supralittoral sandhopper Macarorchestia remyi, a species strictly associated with rotted wood stranded on sand beaches, by analyzing sequence polymorphisms in a fragment of the mitochondrial DNA (mtDNA) gene coding cytochrome oxidase subunit I (COI). The geographical distribution and ecology of the species are poorly known. The study includes 1 Tyrrhenian and 2 Adriatic populations sampled along the Italian peninsula plus a single individual found on Corfu Is. (Greece). The Tyrrhenian population was sampled monthly for 1 yr. Genetic data revealed a deep phylogeographic break between the Tyrrhenian and Adriatic populations with no shared haplotypes. The single individual collected on Corfu Is. carried the most common haplotype found in the Tyrrhenian population. A mismatch analysis could not reject the hypothesis of a sudden demographic expansion in almost all but 2 monthly samples. When compared to previous genetic data centered on a variety of Mediterranean talitrids, our results place M. remyi among those species with profound intraspecific divergence (sandhoppers) and dissimilar from beachfleas, which generally display little population genetic structuring.},
  language  = {en}
}
@article{BonizzoniBourjeaChenetal.2011,
  author    = {Bonizzoni, Mariangela and Bourjea, Jerome and Chen, Bin and Crain, B. J. and Cui, Liwang and Fiorentino, V. and Hartmann, Stefanie and Hendricks, S. and Ketmaier, Valerio and Ma, Xiaoguang and Muths, Delphine and Pavesi, Laura and Pfautsch, Simone and Rieger, M. A. and Santonastaso, T. and Sattabongkot, Jetsumon and Taron, C. H. and Taron, D. J. and Tiedemann, Ralph and Yan, Guiyun and Zheng, Bin and Zhong, Daibin},
  title     = {Permanent genetic resources added to molecular ecology resources database 1 April 2011-31 May 2011},
  series = {Molecular ecology resources},
  volume    = {11},
  journal   = {Molecular ecology resources},
  number    = {5},
  publisher = {Wiley-Blackwell},
  address   = {Malden},
  organization    = {Mol Ecology Resources Primer Dev},
  issn      = {1755-098X},
  doi       = {10.1111/j.1755-0998.2011.03046.x},
  pages     = {935 -- 936},
  year      = {2011},
  abstract  = {This article documents the addition of 92 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anopheles minimus, An. sinensis, An. dirus, Calephelis mutica, Lutjanus kasmira, Murella muralis and Orchestia montagui. These loci were cross-tested on the following species: Calephelis arizonensi, Calephelis borealis, Calephelis nemesis, Calephelis virginiensis and Lutjanus bengalensis.},
  language  = {en}
}
@phdthesis{SammlerKetmaierHavensteinetal.2012,
  author    = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Krause, Ulrike and Curio, Eberhard and Tiedemann, Ralph},
  title     = {Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss},
  doi       = {10.1186/1471-2148-12-203},
  year      = {2012},
  language  = {en}
}
@article{KetmaierMarroneAlfonsoetal.2012,
  author    = {Ketmaier, Valerio and Marrone, Federico and Alfonso, Giuseppe and Paulus, Kirsten B. and Wiemann, Annika and Tiedemann, Ralph and Mura, Graziella},
  title     = {Mitochondrial DNA regionalism and historical demography in the extant populations of chirocephalus kerkyrensis (Branchiopoda: Anostraca)},
  series = {PLoS one},
  volume    = {7},
  journal   = {PLoS one},
  number    = {2},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0030082},
  pages     = {11},
  year      = {2012},
  abstract  = {Background: Mediterranean temporary water bodies are important reservoirs of biodiversity and host a unique assemblage of diapausing aquatic invertebrates. These environments are currently vanishing because of increasing human pressure. Chirocephalus kerkyrensis is a fairy shrimp typical of temporary water bodies in Mediterranean plain forests and has undergone a substantial decline in number of populations in recent years due to habitat loss. We assessed patterns of genetic connectivity and phylogeographic history in the seven extant populations of the species from Albania, Corfu Is. (Greece), Southern and Central Italy. Methodology/Principal Findings: We analyzed sequence variation at two mitochondrial DNA genes (Cytochrome Oxidase I and 16s rRNA) in all the known populations of C. kerkyrensis. We used multiple phylogenetic, phylogeographic and coalescence-based approaches to assess connectivity and historical demography across the whole distribution range of the species. C. kerkyrensis is genetically subdivided into three main mitochondrial lineages; two of them are geographically localized (Corfu Is. and Central Italy) and one encompasses a wide geographic area (Albania and Southern Italy). Most of the detected genetic variation (approximate to 81\%) is apportioned among the aforementioned lineages. Conclusions/Significance: Multiple analyses of mismatch distributions consistently supported both past demographic and spatial expansions with the former predating the latter; demographic expansions were consistently placed during interglacial warm phases of the Pleistocene while spatial expansions were restricted to cold periods. Coalescence methods revealed a scenario of past isolation with low levels of gene flow in line with what is already known for other co-distributed fairy shrimps and suggest drift as the prevailing force in promoting local divergence. We recommend that these evolutionary trajectories should be taken in proper consideration in any effort aimed at protecting Mediterranean temporary water bodies.},
  language  = {en}
}
@article{SilvaIturrizaKetmaierTiedemann2012,
  author    = {Silva-Iturriza, Adriana and Ketmaier, Valerio and Tiedemann, Ralph},
  title     = {Profound population structure in the Philippine Bulbul Hypsipetes philippinus (Pycnonotidae, Ayes) is not reflected in its Haemoproteus haemosporidian parasite},
  series = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics and infectious diseases (MEEGID)},
  volume    = {12},
  journal   = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics and infectious diseases (MEEGID)},
  number    = {1},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1567-1348},
  doi       = {10.1016/j.meegid.2011.10.024},
  pages     = {127 -- 136},
  year      = {2012},
  abstract  = {In this study we used molecular markers to screen for the occurrence and prevalence of the three most common haemosporidian genera (Haemoproteus, Plasmodium, and Leucocytozoon) in blood samples of the Philippine Bulbul (Hypsipetes philippinus), a thrush-size passerine bird endemic to the Philippine Archipelago. We then used molecular data to ask whether the phylogeographic patterns in this insular host-parasite system might follow similar evolutionary trajectories or not. We took advantage of a previous study describing the pattern of genetic structuring in the Philippine Bulbul across the Central Philippine Archipelago (6 islands, 7 populations and 58 individuals; three mitochondrial DNA genes). The very same birds were here screened for the occurrence of parasites by species-specific PCR assays of the mitochondrial cytochrome b gene (471 base pairs). Twenty-eight out of the 58 analysed birds had Haemoproteus (48\%) infections while just 2\% of the birds were infected with either Leucocytozoon or Plasmodium. Sixteen of the 28 birds carrying Haemoproteus had multiple infections. The phylogeography of the Philippine Bulbul mostly reflects the geographical origin of samples and it is consistent with the occurrence of two different subspecies on (1) Semirara and (2) Carabao, Boracay, North Gigante, Panay, and Negros, respectively. Haemoproteus phylogeography shows very little geographical structure, suggesting extensive gene flow among locations. While movements of birds among islands seem very sporadic, we found co-occurring evolutionary divergent parasite lineages. We conclude that historical processes have played a major role in shaping the host phylogeography, while they have left no signature in that of the parasites. Here ongoing population processes, possibly multiple reinvasions mediated by other hosts, are predominant.},
  language  = {en}
}
@article{NahavandiKetmaierTiedemann2012,
  author    = {Nahavandi, Nahid and Ketmaier, Valerio and Tiedemann, Ralph},
  title     = {Intron structure of the elongation factor 1-alpha gene in the ponto-caspian amphipod pontogammarus maeoticus (Sowinsky, 1894) and its phylogeographic utility},
  series = {Journal of crustacean biology},
  volume    = {32},
  journal   = {Journal of crustacean biology},
  number    = {3},
  publisher = {Brill},
  address   = {San Antonio},
  issn      = {0278-0372},
  doi       = {10.1163/193724012X626584},
  pages     = {425 -- 433},
  year      = {2012},
  abstract  = {We tested the utility of a 230 base pair intron fragment of the highly conserved nuclear gene Elongation Factor 1-alpha (EF1-alpha) as a proper marker to reconstruct the phylogeography of the marine amphipod Pontogammarus maeoticus (Sowinsky, 1894) from the Caspian and Black Seas. As a prerequisite for further analysis, we confirmed by Southern blot analysis that EF1-alpha is encoded at a single locus in P. maeoticus. We included 15 populations and 60 individuals in the study. Both the phylogeny of the 27 unique alleles found and population genetic analyses revealed a significant differentiation between populations from the aforementioned sea basins. Our results are in remarkable agreement with recent studies on a variety of species from the same area, which invariably support a major phylogeographic break between the Caspian and Black Seas. We thus conclude that our EF1-alpha intron is an informative marker for phylogeographic studies in amphipods at the shallow population level.},
  language  = {en}
}
@article{SammlerKetmaierHavensteinetal.2012,
  author    = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Krause, Ulrike and Curio, Eberhard and Tiedemann, Ralph},
  title     = {Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss},
  series = {BMC evolutionary biology},
  volume    = {12},
  journal   = {BMC evolutionary biology},
  number    = {25},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2148},
  doi       = {10.1186/1471-2148-12-203},
  pages     = {14},
  year      = {2012},
  abstract  = {Background: The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in similar to 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results: Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions: We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow and population exchange across islands, saving of the remaining birds of almost extinct local populations - be it in the wild or in captivity - is particularly important to preserve the species' genetic potential.},
  language  = {en}
}
@article{SilvaIturrizaKetmaierTiedemann2012,
  author    = {Silva-Iturriza, Adriana and Ketmaier, Valerio and Tiedemann, Ralph},
  title     = {Prevalence of avian haemosporidian parasites and their host fidelity in the central Philippine islands},
  series = {PARASITOLOGY INTERNATIONAL},
  volume    = {61},
  journal   = {PARASITOLOGY INTERNATIONAL},
  number    = {4},
  publisher = {ELSEVIER IRELAND LTD},
  address   = {CLARE},
  issn      = {1383-5769},
  doi       = {10.1016/j.parint.2012.07.003},
  pages     = {650 -- 657},
  year      = {2012},
  abstract  = {We examined the prevalence and host fidelity of avian haemosporidian parasites belonging to the genera Haemoproteus, Leucocytozoon and Plasmodium in the central Philippine islands by sampling 23 bird families (42 species). Using species-specific PCR assays of the mitochondrial cytochrome b gene (471 base pairs, bp), we detected infections in 91 of the 215 screened individuals (42\%). We also discriminated between single and multiple infections. Thirty-one infected individuals harbored a single Haemoproteus lineage (14\%), 18 a single Leucocytozoon lineage (8\%) and 12 a single Plasmodium lineage (6\%). Of the 215 screened birds, 30 (14\%) presented different types of multiple infections. Intrageneric mixed infections were generally more common (18 Haemoproteus/Haemoproteus, 3 Leucocytozoon/Leucocytozoon, and 1 Plasmodium/Plasmodium) than intergeneric mixed infections (7 Haemoproteus/Leucocytozoon and 1 Haemoproteus/Leucocytozoon/Plasmodium). We recovered 81 unique haemosporidian mitochondrial haplotypes. These clustered in three strongly supported monophyletic clades that correspond to the three haemosporidian genera. Related lineages of Haemoproteus and Leucocytozoon were more likely to derive from the same host family than predicted by chance; however, this was not the case for Plasmodium. These results indicate that switches between host families are more likely to occur in Plasmodium. We conclude that Haemoproteus has undergone a recent diversification across well-supported host-family specific clades, while Leucocytozoon shows a longer association with its host(s). This study supports previous evidence of a higher prevalence and stronger host-family specificity of Haemoproteus and Leucocytozoon compared to Plasmodium. (C) 2012 Elsevier Ireland Ltd. All rights reserved.},
  language  = {en}
}
@article{PavesiDeidunDeMatthaeisetal.2012,
  author    = {Pavesi, Laura and Deidun, Alan and De Matthaeis, Elvira and Tiedemann, Ralph and Ketmaier, Valerio},
  title     = {Mitochondrial DNA and microsatellites reveal significant divergence in the beachflea Orchestia montagui (Talitridae: Amphipoda)},
  series = {Aquatic sciences : research across boundaries},
  volume    = {74},
  journal   = {Aquatic sciences : research across boundaries},
  number    = {3},
  publisher = {Springer},
  address   = {Basel},
  issn      = {1015-1621},
  doi       = {10.1007/s00027-012-0250-y},
  pages     = {587 -- 596},
  year      = {2012},
  abstract  = {Talitrids are semiterrestrial crustacean amphipods inhabiting sandy and rocky beaches; they generally show limited active dispersal over long distances. In this study we assessed levels of population genetic structure and variability in the talitrid amphipod Orchestia montagui, a species strictly associated to stranded decaying heaps of the seagrass Posidonia oceanica. The study is based on six populations (153 individuals) and covers five basins of the Mediterranean Sea (Tyrrhenian, Ionian, Adriatic, Western and Eastern basins). Samples were screened for polymorphisms at a fragment of the mitochondrial DNA (mtDNA) coding for the cytochrome oxidase subunit I gene (COI; 571 base pairs) and at eight microsatellite loci. MtDNA revealed a relatively homogeneous haplogroup, which clustered together the populations from the Western, Tyrrhenian and Eastern basins, but not the populations from the Adriatic and Ionian ones; microsatellites detected two clusters, one including the Adriatic and Ionian populations, the second grouping all the others. We found a weak geographic pattern in the genetic structuring of the species, with a lack of isolation by distance at either class of markers. Results are discussed in terms of probability of passive dispersal over long distances through heaps of seagrass.},
  language  = {en}
}
@article{WildishPavesiKetmaier2012,
  author    = {Wildish, J. and Pavesi, Laura and Ketmaier, Valerio},
  title     = {Talitrid amphipods (Crustacea: Amphipoda: Talitridae) and the driftwood ecological niche a morphological and molecular study},
  series = {Journal of natural history : an international journal of systematics, interactive biology and biodiversity. - London : Taylor \& Francis   1.1967 -},
  volume    = {46},
  journal   = {Journal of natural history : an international journal of systematics, interactive biology and biodiversity. - London : Taylor \& Francis   1.1967 -},
  number    = {43-44},
  publisher = {Routledge, Taylor \& Francis Group},
  address   = {Abingdon},
  issn      = {0022-2933},
  doi       = {10.1080/00222933.2012.717971},
  pages     = {2677 -- 2700},
  year      = {2012},
  abstract  = {Coastal regions of the North East Atlantic and Mediterranean Seas have four known species of driftwood talitrids. Records are extremely scanty, often limited to the type locality and dating to 1950. We were able to study three of them, all belonging to the genus Macarorchestia, using fresh and archived samples including type material. Allometric and molecular analyses support: (1) a close relationship among all the three classically defined Macarorchestia species, (2) Macarorchestia was well separated from non-driftwood taxa, and (3) a putative new driftwood talitrid discovered during this study was not closely related to Macarorchestia. Genetic divergence between the new species and Macarorchestia remyi is as high as the average distance among a number of talitrid species included in the study for comparison. A key is provided to identify all three of the presently known species of Macarorchestia, using morphological characters employed in the allometric study.},
  language  = {en}
}
@article{NahavandiKetmaierPlathetal.2013,
  author    = {Nahavandi, Nahid and Ketmaier, Valerio and Plath, Martin and Tiedemann, Ralph},
  title     = {Diversification of Ponto-Caspian aquatic fauna - morphology and molecules retrieve congruent evolutionary relationships in Pontogammarus maeoticus (Amphipoda: Pontogammaridae)},
  series = {Molecular phylogenetics and evolution},
  volume    = {69},
  journal   = {Molecular phylogenetics and evolution},
  number    = {3},
  publisher = {Elsevier},
  address   = {San Diego},
  issn      = {1055-7903},
  doi       = {10.1016/j.ympev.2013.05.021},
  pages     = {1063 -- 1076},
  year      = {2013},
  abstract  = {The geological history of the Ponto-Caspian region, with alternating cycles of isolation and reconnection among the three main basins (Black and Azov Seas, and the more distant Caspian Sea) as well as between them and the Mediterranean Sea, profoundly affected the diversification of its aquatic fauna, leading to a high degree of endemism. Two alternative hypotheses on the origin of this amazing biodiversity have been proposed, corresponding to phases of allopatric separation of aquatic fauna among sea basins: a Late Miocene origin (10-6 MYA) vs. a more recent Pleistocene ancestry (<2 MYA). Both hypotheses support a vicariant origin of (1) Black + Azov Sea lineages on the one hand, and (2) Caspian Sea lineages on the other. Here, we present a study on the Ponto-Caspian endemic amphipod Pontogammarus maeoticus. We assessed patterns of divergence based on (a) two mitochondrial and one nuclear gene, and (b) a morphometric analysis of 23 morphological traits in 16 populations from South and West Caspian Sea, South Azov Sea and North-West Black Sea. Genetic data indicate a long and independent evolutionary history, dating back from the late Miocene to early Pleistocene (6.6-1.6 MYA), for an unexpected, major split between (i) a Black Sea clade and (ii) a well-supported clade grouping individuals from the Caspian and Azov Seas. Absence of shared haplotypes argues against either recent or human-mediated exchanges between Caspian and Azov Seas. A mismatch distribution analysis supports more stable population demography in the Caspian than in the Black Sea populations. Morphological divergence largely followed patterns of genetic divergence: our analyses grouped samples according to the basin of origin and corroborated the close phylogenetic affinity between Caspian and Azov Sea lineages. Altogether, our results highlight the necessity of careful (group-specific) evaluation of evolutionary trajectories in marine taxa that should certainly not be inferred from the current geographical proximity of sea basins alone. (C) 2013 Elsevier Inc. All rights reserved.},
  language  = {en}
}
@misc{SammlerKetmaierHavensteinetal.2013,
  author    = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Tiedemann, Ralph},
  title     = {Intraspecific rearrangement of duplicated mitochondrial control regions in the luzon tarictic hornbill penelopides manillae (Aves: Bucerotidae)},
  series = {Journal of molecular evolution},
  volume    = {77},
  journal   = {Journal of molecular evolution},
  number    = {5-6},
  publisher = {Springer},
  address   = {New York},
  issn      = {0022-2844},
  doi       = {10.1007/s00239-013-9591-y},
  pages     = {199 -- 205},
  year      = {2013},
  abstract  = {Philippine hornbills of the genera Aceros and Penelopides (Bucerotidae) are known to possess a large tandemly duplicated fragment in their mitochondrial genome, whose paralogous parts largely evolve in concert. In the present study, we surveyed the two distinguishable duplicated control regions in several individuals of the Luzon Tarictic Hornbill Penelopides manillae, compare their characteristics within and across individuals, and report on an intraspecific mitochondrial gene rearrangement found in one single specimen, i.e., an interchange between the two control regions. To our knowledge, this is the first observation of two distinct mitochondrial genome rearrangements within a bird species. We briefly discuss a possible evolutionary mechanism responsible for this pattern, and highlight potential implications for the application of control region sequences as a marker in population genetics and phylogeography.},
  language  = {en}
}
@article{PavesiTiedemannDeMatthaeisetal.2013,
  author    = {Pavesi, Laura and Tiedemann, Ralph and DeMatthaeis, Elvira and Ketmaier, Valerio},
  title     = {Genetic connectivity between land and sea: the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea},
  issn      = {1742-9994},
  year      = {2013},
  language  = {en}
}
@article{PavesiTiedemannDeMatthaeisetal.2013,
  author    = {Pavesi, Laura and Tiedemann, Ralph and De Matthaeis, Elvira and Ketmaier, Valerio},
  title     = {Genetic connectivity between land and sea - the case of the beachflea Orchestia montagui (Crustacea, Amphipoda, Talitridae) in the Mediterranean Sea},
  series = {Frontiers in zoology},
  volume    = {10},
  journal   = {Frontiers in zoology},
  number    = {4-5},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1742-9994},
  doi       = {10.1186/1742-9994-10-21},
  pages     = {19},
  year      = {2013},
  abstract  = {Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces. Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set. Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.},
  language  = {en}
}
@misc{PavesiTiedemannDeMatthaeisetal.2013,
  author    = {Pavesi, Laura and Tiedemann, Ralph and De Matthaeis, Elvira and Ketmaier, Valerio},
  title     = {Genetic connectivity between land and sea},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401110},
  pages     = {19},
  year      = {2013},
  abstract  = {Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces. Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set. Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.},
  language  = {en}
}
@article{ZarattiniMuraKetmaier2013,
  author    = {Zarattini, Paola and Mura, Graziella and Ketmaier, Valerio},
  title     = {Intra-specific variability in the thirteen known populations of the fairy shrimp Chirocephalus ruffoi (Crustacea: Anostraca) - resting egg morphometrics and mitochondrial DNA reveal decoupled patterns of deep divergence},
  series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  volume    = {713},
  journal   = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0018-8158},
  doi       = {10.1007/s10750-013-1487-8},
  pages     = {19 -- 34},
  year      = {2013},
  abstract  = {Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (a parts per thousand 70\%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans.},
  language  = {en}
}
@unpublished{LoBruttoArculeoKrappSchickeletal.2013,
  author    = {Lo Brutto, Sabrina and Arculeo, Marco and Krapp-Schickel, Traudl and Ketmaier, Valerio},
  title     = {Foreword to the special issue "New frontiers for monitoring european biodiversity - the role and importance of amphipod crustaceans"},
  series = {Crustaceana : international journal of crustacean research},
  volume    = {86},
  journal   = {Crustaceana : international journal of crustacean research},
  number    = {7-8},
  publisher = {Brill},
  address   = {Leiden},
  issn      = {0011-216X},
  doi       = {10.1163/15685403-00003204},
  pages     = {769 -- 779},
  year      = {2013},
  language  = {en}
}
@article{PavesiKetmaier2013,
  author    = {Pavesi, Laura and Ketmaier, Valerio},
  title     = {Patterns of genetics structuring and levels of differentiation in supralittoral talitrid amphipods - an overview},
  series = {Crustaceana : international journal of crustacean research},
  volume    = {86},
  journal   = {Crustaceana : international journal of crustacean research},
  number    = {7-8},
  publisher = {Brill},
  address   = {Leiden},
  issn      = {0011-216X},
  doi       = {10.1163/15685403-00003212},
  pages     = {890 -- 907},
  year      = {2013},
  abstract  = {Talitrids are the only family within the order Amphipoda to have colonised supralittoral and terrestrial environments. They live in a variety of settings, from sandy to rocky and pebble beaches, to river and lake banks, and to leaf litter and caves. A common feature is the absence of a planktonic larval stage to facilitate passive dispersal over long-distances. However, some species have broad distributions. Genetic studies over the past 25 years have tried to explain this apparent contradiction by assessing patterns of species genetic structuring on different geographical scales. Here, we review the molecular studies available to date and focus on the population genetics of talitrids. Most of these studies considered populations in the Mediterranean area, but also along the Atlantic coast and in Canary Island caves. From this review, the group emerges as a potential model to understand processes of dispersal and divergence in non-highly-vagile supralittoral organisms. At the same time, studies on these issues are still too restricted geographically: a worldwide scale including different regions would provide us with a better perspective on these problems.},
  language  = {en}
}
@article{TaylanDiRussoRampinietal.2013,
  author    = {Taylan, Mehmet Sait and Di Russo, Claudio and Rampini, Mauro and Ketmaier, Valerio},
  title     = {Molecular systematics of the genus Troglophilus (Rhaphidophoridae, Orthoptera) in Turkey mitochondrial 16S rDNA evidences},
  series = {ZooKeys},
  journal   = {ZooKeys},
  number    = {257},
  publisher = {Pensoft Publ.},
  address   = {Sofia},
  issn      = {1313-2989},
  doi       = {10.3897/zookeys.257.4133},
  pages     = {33 -- 46},
  year      = {2013},
  abstract  = {This study focuses on the evolutionary relationships among Turkish species of the cave cricket genus Troglophilus. Fifteen populations were studied for sequence variation in a fragment (543 base pairs) of the mitochondrial DNA (mtDNA) 16S rDNA gene (16S) to reconstruct their phylogenetic relationships and biogeographic history. Genetic data retrieved three main clades and at least three divergent lineages that could not be attributed to any of the taxa known for the area. Molecular time estimates suggest that the diversification of the group took place between the Messinian and the Plio-Pleistocene.},
  language  = {en}
}
@article{BiancoKetmaier2014,
  author    = {Bianco, Pier Giorgio and Ketmaier, Valerio},
  title     = {A revision of the Rutilus complex from Mediterranean Europe with description of a new genus, Sarmarutilus, and a new species, Rutilus stoumboudae (Teleostei: Cyprinidae)},
  series = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists},
  volume    = {3841},
  journal   = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists},
  number    = {3},
  publisher = {Magnolia Press},
  address   = {Auckland},
  issn      = {1175-5326},
  pages     = {379 -- 402},
  year      = {2014},
  abstract  = {By combining morphology, ecology, biology, and biogeography with the available molecular (sequence variation of the entire mitochondrial cytochrome b gene; cyt-b) and karyology data, the taxonomy of several species of the Rutilus complex inhabiting southern Europe is revised. Rutilus stoumboudae, new species, is described from Lake Volvi, Greece. It differs from Rutilus rutilus in possessing more total GR and less branched rays in both dorsal and anal fins and in its placement in the cyt-b based phylogeny of the genus. The resurrected genus Leucos Heckel, 1843 (type species Leucos aula, Bonaparte, 1841), which according to molecular data diverged from Rutilus more than 5 million years ago, during the Messinian salinity crisis, includes five species of small size, without spinous tubercles on scales and head in reproductive males, pharyngeal teeth formula 5-5, and all show a preference for still waters. Leucos aula is the Italian species endemic in the Padany-Venetian district: L. basak is widespread in Croatia, Albania, Montenegro and former Yugoslav Republic of Macedonia (FYROM); L. albus, recently described from Lake Skadar, Montenegro, is also found in rivers Moraca and Zeta (Montenegro). L. albus differs from L. basak, its closest relative, in having more scales on the LL and less anal-fin rays; L. panosi is endemic to the western-Greece district, and L. ylikiensis is endemic to lakes Yliki and Paralimni in eastern Greece (introduced in Lake Volvi). Among the nominal species examined, Rutilus karamani, R. ohridanus, R. prespensis and R. prespensis vukovici are all junior synonyms of Leucos basak. Rutilus vegariticus is definitively regarded as junior synonym for R. rutilus. Sarmarutilus n.gen. is a monotypic genus, with Sarmarutilus rubilio as the type species. According to phylogenetic data, Sarmarutilus rubilio is basal to a cluster of species that includes Leucos basak, L. albus, L. aula, L. panosi and L. ylikiensis. Sarmarutilus possibly evolved in pre-Messinian time, in the Lago Mare, entered the Mediterranean area during the Messinian Lago Mare phase of the Mediterranean Sea and survived only in the Tuscany-Latium district. This genus differs from Leucos in having large pearl organs on the central part of head and body scales in mature males and for the habitat preference, being a riverine-adapted species. It differs from Rutilus in pharyngeal teeth formula (5-5 in Sarmarutilus and 6-5 in Rutilus), size (small in Sarmarutilus and large in Rutilus) and for the preferential habitat (riverine vs. still water). Finally, lectotypes for Leucos basak, Leucos aula, and Sarmarutilus rubilio are designated.},
  language  = {en}
}
@article{SchedinaPfautschHartmannetal.2014,
  author    = {Schedina, Ina-Maria and Pfautsch, Simone and Hartmann, Stefanie and Dolgener, N. and Polgar, Anika and Bianco, Pier Giorgio and Tiedemann, Ralph and Ketmaier, Valerio},
  title     = {Isolation and characterization of eight microsatellite loci in the brook lamprey Lampetra planeri (Petromyzontiformes) using 454 sequence data},
  series = {Journal of fish biology},
  volume    = {85},
  journal   = {Journal of fish biology},
  number    = {3},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0022-1112},
  doi       = {10.1111/jfb.12470},
  pages     = {960 -- 964},
  year      = {2014},
  abstract  = {Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0.388 and 0.424 and a mean observed heterozygosity of 0.418 and 0.411, respectively. (C) 2014 The Fisheries Society of the British Isles},
  language  = {en}
}
@article{SbragagliaLamannaMatetal.2015,
  author    = {Sbragaglia, Valerio and Lamanna, Francesco and Mat, Audrey M. and Rotllant, Guiomar and Joly, Silvia and Ketmaier, Valerio and de la Iglesia, Horacio O. and Aguzzi, Jacopo},
  title     = {Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk},
  series = {PLoS one},
  volume    = {10},
  journal   = {PLoS one},
  number    = {11},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0141893},
  pages     = {17},
  year      = {2015},
  abstract  = {The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12-12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47\%, timeless: 59\%, bmal1: 79\%) and Macrobrachium rosenbergii (clock: 100\%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster.},
  language  = {en}
}
@article{SbragagliaLamannaMatetal.2015,
  author    = {Sbragaglia, Valerio and Lamanna, Francesco and Mat, Audrey M. and Rotllant, Guiomar and Joly, Silvia and Ketmaier, Valerio and de la Iglesia, Horacio O. and Aguzzi, Jacopo},
  title     = {Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk},
  series = {PLoS one},
  volume    = {10},
  journal   = {PLoS one},
  number    = {11},
  publisher = {Public Library of Science},
  address   = {Lawrence},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0141893},
  year      = {2015},
  abstract  = {The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12-12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47\%, timeless: 59\%, bmal1: 79\%) and Macrobrachium rosenbergii (clock: 100\%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster.},
  language  = {en}
}
@misc{SbragagliaLamannaMatetal.2015,
  author    = {Sbragaglia, Valerio and Lamanna, Francesco and Mat, Audrey M. and Rotllant, Guiomar and Joly, Silvia and Ketmaier, Valerio and de la Iglesia, Horacio O. and Aguzzi, Jacopo},
  title     = {Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-84432},
  year      = {2015},
  abstract  = {The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12-12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47\%, timeless: 59\%, bmal1: 79\%) and Macrobrachium rosenbergii (clock: 100\%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster.},
  language  = {en}
}
@misc{SammlerKetmaierHavensteinetal.2017,
  author    = {Sammler, Svenja and Ketmaier, Valerio and Havenstein, Katja and Krause, Ulrike and Curio, Eberhard and Tiedemann, Ralph},
  title     = {Mitochondrial control region I and microsatellite analyses of endangered Philippine hornbill species (Aves; Bucerotidae) detect gene flow between island populations and genetic diversity loss},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-401108},
  pages     = {14},
  year      = {2017},
  abstract  = {Background: The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in similar to 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species. Results: Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations. Conclusions: We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow and population exchange across islands, saving of the remaining birds of almost extinct local populations - be it in the wild or in captivity - is particularly important to preserve the species' genetic potential.},
  language  = {en}
}
@article{DeCahsanNagelSchedinaetal.2020,
  author    = {De Cahsan, Binia and Nagel, Rebecca and Schedina, Ina-Maria and King, James J. and Bianco, Pier G. and Tiedemann, Ralph and Ketmaier, Valerio},
  title     = {Phylogeography of the European brook lamprey (Lampetra planeri) and the European river lamprey (Lampetra fluviatilis) species pair based on mitochondrial data},
  series = {Journal of fish biology},
  volume    = {96},
  journal   = {Journal of fish biology},
  number    = {4},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {0022-1112},
  doi       = {10.1111/jfb.14279},
  pages     = {905 -- 912},
  year      = {2020},
  abstract  = {The European river lamprey Lampetra fluviatilis and the European brook lamprey Lampetra planeri (Block 1784) are classified as a paired species, characterized by notably different life histories but morphological similarities. Previous work has further shown limited genetic differentiation between these two species at the mitochondrial DNA level. Here, we expand on this previous work, which focused on lamprey species from the Iberian Peninsula in the south and mainland Europe in the north, by sequencing three mitochondrial marker regions of Lampetra individuals from five river systems in Ireland and five in southern Italy. Our results corroborate the previously identified pattern of genetic diversity for the species pair. We also show significant genetic differentiation between Irish and mainland European lamprey populations, suggesting another ichthyogeographic district distinct from those previously defined. Finally, our results stress the importance of southern Italian L. planeri populations, which maintain several private alleles and notable genetic diversity.},
  language  = {en}
}