New distribution data and population structure of the European mudminnow Umbra krameri in Serbia and Bosnia and Herzegovina

Seventy‐six individuals of the European mudminnow Umbra krameri from two recent populations from Serbia (Bakreni Batar and Lugomir) and one from Bosnia and Herzegovina (Gromi?elj) were analysed for habitat preferences and population structure. The population from Lugomir is a newly recorded population in Serbia. Besides this new record, it is noteworthy that all three studied locations are outside the currently known species distribution range limits.     

Phylogeographic analysis reveals northerly refugia for the riverine amphibian Triturus dobrogicus (Caudata: Salamandridae)

We investigated the recent evolutionary history of the Danube crested newt, Triturus dobrogicus through reconstructions of: (1) the number and position of refugia at the last glacial maximum, (2) the role of major central European rivers in pattern of post‐glacial dispersal, and (3) the present‐day distribution pattern. We analysed sequences of mitochondrial DNA (ND2, 1065 bp) and six microsatellite loci in 363 T. dobrogicus individuals from 58 populations covering the range of the species. Our analyses suggested that T. dobrogicus survived the last glacial maximum in two separate refugia positioned in northwestern Pannonia and in Southern Pannonia from where its range expanded along the Danube and Tisza Rivers. Our findings also confirmed that rivers played an important role in shaping the evolutionary history of amphibian species in Central Europe. We compared the T. dobrogicus range with another lowland amphibian, the fire‐bellied toad Bombina bombina, using species distribution modelling. In line with these models, the isolated mountains inside Pannonia are occupied not by B. bombina, but by its mountain‐dwelling sister‐species B. variegata. However, in contrast to the model, crested newts (including T. dobrogicus) are absent from these mountains. We attribute this biogeographical discrepancy to the positioning of the species’ refugia at the last glacial maximum.     

Morphologic and genetic variability in the Barbus fishes (Teleostei,Cyprinidae) of Central Italy

Italian freshwaters are highly biodiverse, with species present including the native fishes Barbus plebejus and Barbus tyberinus that are threatened by habitat alteration, fish stocking and invasive fishes, especially European barbel Barbus barbus. In central Italy, native fluvio‐lacustrine barbels are mainly allopatric and so provide an excellent natural system to evaluate the permeability of the Apennine Mountains. Here, the morphologic and genetic distinctiveness was determined for 611 Barbus fishes collected along the Padany–Venetian (Adriatic basins; PV) and Tuscany–Latium (Tyrrhenian basins; TL) districts. Analyses of morphological traits and mitochondrial DNA sequence data explored the natural and anthropogenic factors that have shaped their distribution ranges. Over 100 alien B. barbus were recorded in the Tiber basin (TL district) and Metauro basin (PV district). Comparisons of genetic and morphometric data revealed that morphometric data could identify alien B. barbus from native Barbus, but could not differentiate between B. tyberinus and B. plebejus. Genetic analyses revealed ~50 D‐loop mtDNA haplotypes and identified a distinct Barbus lineage present only in the Vomano River at the southern boundary of PV district. Demographic expansion and molecular variance analyses revealed a lack of geographic structuring across the sampling regions. While the contemporary B. plebejus distribution has been driven primarily by anthropogenic fish translocations, the dispersal of B. tyberinus has been via natural dispersion, including their crossing of the Apennine Mountains via temporary river connectivity. The results also revealed that the Barbus fishes of the mid‐Adriatic region of Europe have a complex pattern of local endemism. To conserve these patterns of genetic uniqueness, especially in the mid‐Adriatic basins, Barbus fishes should be managed by treating them as unique evolutionary units and ceasing translocations of all Barbus fishes between river basins.     

Genetic admixture of burbot (Teleostei: Lota lota) in Lake Constance from two European glacial refugia

The burbot, Lota lota, is the only freshwater species of the codfish family and has a Holarctic distribution. Pleistocene glaciations caused significant geographical differentiation in the past, but its life history characterized by winter spawning migrations over large distances is likely to homogenize populations by contemporary gene flow. We investigated the population genetic structure of 541 burbots from Lake Constance and adjacent Rhine and Danube tributaries in Europe using the entire mitochondrial DNA (mtDNA) control region and 11 microsatellites. Microsatellites revealed considerable population divergence (F(ST) = 0.26) and evidenced recent bottlenecks in two Central European rivers. In accordance to previous evidence two main phylogeographic lineages (Atlantic and Danubian) were found co-occurring at similar frequencies in Lake Constance, where they currently undergo random mating as indicated by microsatellites. The Danubian lineage contributed only a small proportion to the lake's mtDNA diversity, and probably expanded within the lake shortly after its formation approximately 10,000-15,000 BP. The larger Atlantic haplotype diversity suggested a population expansion older than the lake itself. Levels of admixture at microsatellite loci were less obvious due to their high variability, and coalescence methods were used to estimate past admixture proportions. Our results reinforce a model of a two-step colonization of Europe by burbot from an ancestral Danubian refuge, and confirm the persistence of a secondary Atlantic refuge, as proposed to exist for other freshwater fish. We conclude that the present-day burbot population in Lake Constance bears the genetic signature of both contemporary gene flow and historical separation events.     

Genetic and morphological characterization of the freshwater mussel clubshell species complex (Pleurobema clava and Pleurobema oviforme) to inform conservation planning

The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species'' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.     

Leaf morphological analyses in four European oak species (Quercus) and their hybrids: A comparison of traditional and geometric morphometric methods

Abstract

In this study, leaf morphology was assessed in a mixed oak stand (western France) using two geometric morphometric (landmark and outline) datasets and one dataset of 19 leaf measures. Adult oaks (817 oaks), comprising four white oak species (Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica), were sampled for DNA extraction and genetic analysis (nuclear microsatellites). Leaf morphology was assessed on 336 oaks, comprising pure species and hybrids as determined by genetic assignment. This comparative study of oak leaf morphology, based on the use of two free size geometric morphometric methods and a set of leaf measurements, combined with the genetic assignment of individuals to pure species or hybrids, provided information about the differences among species and the intermediate leaf morphology of their hybrids.     

Habitat use of the European mudminnow Umbra krameri and association with other fish species in a disconnected Danube side arm

Fish assemblages along the longitudinal course of an old, disconnected and modified side arm of the Danube floodplain downstream of Vienna, Austria, as well as habitat structure, hydro‐morphological and hydro‐chemical factors, were investigated in order to analyse the key environmental determinants of the European mudminnow Umbra krameri. Generally, U. krameri was the most abundant species in the system. It occurred in disconnected ditches, ponds and pools with dense reed belts and comparatively low nutrient content, indicating its natural association with marsh habitats. At infrequently disturbed sites it was associated with a small group of stagnophilious and highly specialized species with adaptations to strong oxygen fluctuations. At frequently flooded sites, the species was absent or occurred in low abundances, indicating its adaptation to water bodies in older successional stages and its low competitive power in permanently connected floodplain habitats.     

Adaptive radiation in African weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and morphological approach

We combined multiple molecular markers and geometric morphometrics to revise the current taxonomy and to build a phylogenetic hypothesis for the African weakly electric fish genus Campylomormyrus. Genetic data (2039 bp DNA sequence of mitochondrial cytochrome b and nuclear S7 genes) on 106 specimens support the existence of at least six species occurring in sympatry. We were able to further confirm these species by microsatellite analysis at 16 unlinked nuclear loci and landmark-based morphometrics. We assigned them to nominal taxa by comparisons to type specimens of all Campylomormyrus species recognized so far. Additionally, we showed that the shape of the elongated trunk-like snout is the major source of morphological differentiation among them. This finding suggests that the radiation of this speciose genus might have been driven by adaptation to different food sources.     

Genetic diversity and morphological variability in the Balkan endemic Campanula secundiflora s.l. (Campanulaceae)

We reconstructed the relationships among populations of Campanula secundiflora s.l. and closely related and geographically close populations of C. austroadriatica and C. versicolor. Based on analyses of microsatellite DNA data, the investigated populations have high overall genetic diversity and abundant allelic variation over seven investigated loci. Bayesian model‐based clustering identified four clearly differentiated genetic groups of populations. The genetic differentiation was reflected by morphological differentiation, allowing us to propose a new taxonomic treatment of the constituents of C. secundiflora s.l. The populations distributed in south‐western Serbia and north‐eastern Montenegro were included in C. secundiflora. A new species, C ampanula montenegrina sp. nov. , distributed in the continental part of Montenegro and the northern part of Albania is described. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2016, 180 , 64–88.     

Genetic and morphological variability of the endangered Syngonanthus mucugensis Giul. (Eriocaulaceae) from the Chapada Diamantina, Brazil: implications for conservation and taxonomy

Allozymic and morphometric studies were carried out on ten populations of Syngonanthus mucugensis (Eriocaulaceae), a species from north-eastern Brazil threatened by extinction. Genetic and morphological variability was low or moderately low in all populations, being lower in populations from Rio de Contas/Catolés ( P _L = 14.3–21.4, A  = 1.1–1.2, H _e = 0.026–0.059, D2M = 26.893–33.157) than in those from Mucugê ( P _L = 28.6–35.7, A  = 1.3–1.5, H _e = 0.078–0.164, D2M = 28.999–45.077). A high coefficient of endogamy ( F _is = 0.257) was found, which can be explained by the reproductive characteristics and distribution of the species. The values for genetic and morphological structuring ( F _st = 0.512 and A _MRPP = 0.175, respectively) were high as a result of the differentiation between populations from the two areas. The mean genetic identity between populations from the two areas (0.812) was much lower than between populations from the same area (Mucugê, 0.980; Rio de Contas/Catolés, 0.997). These results indicate that we are dealing with two distinct taxa and, as a result of the nature of the morphological differences found, a new subspecies is described for the populations of the region of Rio de Contas and Catolés, Syngonanthus mucugensis ssp. riocontensis . Such conclusions raise important implications for the conservation of Syngonanthus mucugensis , and will be used in the drawing up of management plans for its conservation.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 401–416.     

Population Genetic Patterns of Threatened European Mudminnow (Umbra krameri Walbaum, 1792) in a Fragmented Landscape: Implications for Conservation Management

The European mudminnow (Umbra krameri) is a Middle Danubian endemic fish species, which is characterised by isolated populations living mainly in artificial habitats in the centre of its range, in the Carpathian Basin. For their long term preservation, reliable information is needed about the structure of stocks and the level of isolation. The recent distribution pattern, and the population genetic structure within and among regions were investigated to designate the Evolutionary Significant, Conservation and Management Units (ESUs, CUs, MUs) and to explore the conservation biological value of the shrinking populations. In total, eight microsatellite loci were studied in 404 specimens originating from eight regions. The results revealed a pronounced population structure, where strictly limited gene flow was detected among regions, as well as various strengths of connections within regions. Following the results of hierarchical structure analyses, two ESUs were supposed in the Carpathian Basin, corresponding to the Danube and Tisza catchments. Our results recommend designating the borders of CUs in an 80–90km range and 16 clusters should be set up as MUs for the 33 investigated populations. How these genetic findings can be used to better allocate conservation resources for the long term maintenance of the metapopulation structure of this threathened endemic fish is discussed.     

Interpopulation genetic divergence in European grayling (Thymallus thymallus, Salmonidae) at a microgeographic scale: implications for conservation

In order to provide guidelines for conservationand management of the severely declining LakeSaimaa (eastern Finland) European grayling(Thymallus thymallus, Salmonidae), weinvestigated the microgeographic geneticstructure of three populations from the watersystem using 17 microsatellite loci andmitochondrial DNA polymerase chainreaction-restriction fragment lengthpolymorphism analysis. Microsatellites revealedlow levels of intrapopulation genetic diversityand substantial divergence between populationssampled from spawning sites separated by aslittle as 55 kilometers. Mitochondrial analysisindicated the occurrence of two compositehaplotypes within Lake Saimaa. The nucleotidesubstitution estimates between the haplotypessuggested their separation to markedly predatethe late Pleistocene period. The populationsexhibited marked frequency differences for thetwo mitochondrial haplotypes, reinforcing theview of limited interpopulation gene flowwithin Lake Saimaa. An individual basedmicrosatellite Neighbor-Joining dendrogramdemonstrated clustering of all the specimensaccording to their sampling origin. Individualassignment tests revealed 100% assignmentsuccess of individuals into their population oforigin and 100% exclusion (p <0.05) from all alternative referencepopulations. These findings exemplify that T. thymallus populations may be genetically highly structured over small geographical scales and provide a good starting point for the development of appropriate conservation strategies for Lake Saimaa grayling.     

Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae)

The jaguar (Panthera onca), the largest felid in the American Continent, is currently threatened by habitat loss, fragmentation and human persecution. We have investigated the genetic diversity, population structure and demographic history of jaguars across their geographical range by analysing 715 base pairs of the mitochondrial DNA (mtDNA) control region and 29 microsatellite loci in approximately 40 individuals sampled from Mexico to southern Brazil. Jaguars display low to moderate levels of mtDNA diversity and medium to high levels of microsatellite size variation, and show evidence of a recent demographic expansion. We estimate that extant jaguar mtDNA lineages arose 280 000-510 000 years ago (95% CI 137 000-830 000 years ago), a younger date than suggested by available fossil data. No strong geographical structure was observed, in contrast to previously proposed subspecific partitions. However, major geographical barriers such as the Amazon river and the Darien straits between northern South America and Central America appear to have restricted historical gene flow in this species, producing measurable genetic differentiation. Jaguars could be divided into four incompletely isolated phylogeographic groups, and further sampling may reveal a finer pattern of subdivision or isolation by distance on a regional level. Operational conservation units for this species can be defined on a biome or ecosystem scale, but should take into account the historical barriers to dispersal identified here. Conservation strategies for jaguars should aim to maintain high levels of gene flow over broad geographical areas, possibly through active management of disconnected populations on a regional scale.     

The phylogenetic structure of habitat shift and morphological convergence in Asian Clarias (Teleostei, Siluriformes: Clariidae)

Catfishes of the genus Clarias are an important component of the ichthyofauna in Asia and in Africa. Previous studies demonstrated a high diversity in number of species, morphology and habitat, but little was known on the evolutionary processes underlying this diversity. We analysed an original data set of molecular sequences (cytochrome b and 16S genes), habitat and geographic distributions, as well as 29 morphometric measurements taken on 454 specimens of Asian Clarias . Maximum likelihood phylogeny estimation showed an unexpected cryptic diversity due to strong morphological convergence. The patterns of intra- and interspecific phylogenetic divergence are overall explained by geographic isolation. The analysis of habitat transitions with Markovian models showed that Asian Clarias evolved from an ancestor probably living in clear waters. The most frequent transitions occurred between clear and white waters, whereas transitions towards black waters occurred only from clear waters and were rare events. The morphometric analysis suggests a complex pattern of morphological evolution with repeated convergence towards an elongated form in black waters. The phylogeographic patterns of diversification of Asian Clarias agree with previous studies on other groups and the hypothesis that changes in sea level during the Pleistocene had little influence on shaping biodiversity on the Sunda Shelf.     

Possible Reason for the Expansion of Carassius auratus (Linnaeus, 1758) (Teleostei,Cyprinidae) in the Danube River Basin

The author found quite a close negative relationship between commercial catches of predatory fishes and of German carp (Carassius auratus) in the lower Danube. He supposes that the main reason for the population explosion and subsequent expansion of German carp in the Danube River basin seems to be a shift in the balance of the fish community due to a reduction in the density of predatory species.     

Island Populations, Human Introductions and the Limitations of Genetic Analyses: the Case of the Sardinian Red Deer (Cervus elaphus corsicanus)

The Corsican red deer (Cervus elaphus corsicanus) is endemic to the Tyrrhenian islands of Corsica and Sardinia. It has been regarded as an introduced species and has allegedly been present on the islands since the beginning of the Neolithic culture some 8,000 years ago. In this review, we present the results of relevant genetic analyses and discuss their implications for the origin of C. e. corsicanus. Different genetic studies hypothesize that the most probable ancestral populations for Sardianian red deer were alternatively, the Near East, North Africa, or mainland Italy. These respective scenarios are evaluated and it is concluded that geneticists have not yet been unable to definitively solve the problem. However, a natural colonization of the Tyrrhenian islands from mainland Italy via the Tuscan archipelago is not only in accordance with palaeontological findings but also with at least some of the genetic data.     

Genetic variability in a captive herd of Speke's gazelle (Gazella spekei)

A captive herd of Speke' gazelle was screened for genetic variability at 28 enzyme-coding loci, the nuclear ribosomal DNA (rDNA), and the mitochondrial DNA (mtDNA). There is one variable restriction site out of 52 in the rDNA and three variable sites out of 41 in the mtDNA. This amount of mitochondrial diversity is low for a mammal, but is about the maximum to be expected given that the entire herd is derived from three females. However, 14% of the enzymecoding loci were polymorphic, a figure typical for mammals. Hence, despite the fact that the herd was founded by one male and three females, much genetic variation is still present. It is therefore important to continue breeding programs designed to maintain genetic diversity. MtDNA is maternally inherited, so tracing back from the current animals through females allowed us to infer that each founding female had a distinct mtDNA haplotype. Hence, the founding females could not have shared the same mother. The nuclear variability could also be traced back through the pedigrees to the founders. One female was found to have contributed none of the assayed genetic variability to the current herd. “Gene drop” simulations of the herd indicated that this was the only founder for which much genetic variability had already been lost because of breeding decisions made during the early history of the herd. This illustrates the importance of implementing breeding programs designed to preserve genetic variability as soon as possible.