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This study deals with the biodiversity and distribution of cavernicolous Amphipoda in caves of the Arabika massif (Western Caucasus). The Sarma, Trojka and Orlinoe Gnezdo caves were explored during speleological expeditions over the years 2011–12. Two new species of Amphipoda were found: a sub-surface dweller Zenkevitchia sandroruffoi sp. nov. is reported from the Sarma, Trojka and Orlinoe Gnezdo caves at depths from -30 m to -350 m; the second one, a deep dweller Adaugammarus pilosus gen. et sp. nov. is reported from the Sarma Cave at depths of -1270 to -1700 m. Adaugammarus gen. nov. shares similarities with Typhlogammarus Schäferna, 1907 and Zenkevitchia Birstein, 1940. The species Anopogammarus birsteini Derzhavin, 1945 is also re-described herein based on new samples that suggest close affinity of this species with the family Gammaridae. The original taxonomic combination is resurrected for Zenkevitchia revazi Birstein & Ljovuschkin, 1970, comb. resurr. (from Anopogammarus Derzhavin, 1945). To accommodate morphologically different species in the genus Zenkevitchia, two new groups are proposed. These are the admirabilis-group (Z. admirabilis Birstein, 1940 and Z. yakovi Sidorov, 2015) and the sandroruffoi-group (Z. sandroruffoi sp. nov. and Z. revazi). An updated molecular (mt-cox1) phylogeny, an identification key to the genera and a distribution map for the typhlogammarid amphipod species of Transcaucasia are provided.
Here I analyse 23 populations of D. galeata, a large-lake cladoceran, distributed mainly across the Palaearctic. I detected high levels of clonal diversity and population differentiation using variation at six microsatellite loci across Europe. Most populations were characterised by deviations from H-W equilibrium and significant heterozygote deficiencies. Observed heterozygote deficiencies might be a consequence of simultaneous hatching of individuals produced during different times of the year or of the coexistence of ecologically and genetically differentiated subpopulations. A significant isolation by distance was only found over large geographic distances (> 700 km). This pattern is mainly due to the high genetic differentiation among neighbouring populations. My results suggest that historic populations of Daphnia were once interconnected by gene flow but current populations are now largely isolated. Thus local ecological conditions which determine the level of biparental sexual reproduction and local adaptation are the main factors mediating population structure of D. galeata. The population genetic structure and diversity in D. galeata was investigated at a European scale using six microsatellite loci and 12S rDNA sequence data to infer and compare historical and contemporary patterns of gene flow. D. galeata has the potential for long-distance dispersal via ephippial resting eggs by wind and other dispersing vectors (waterfowl), but shows in general strong population differentiation even among neighbouring populations. A total of 427 individuals were analysed for microsatellite and 85 individuals for mitochondrial (mtDNA) sequence data from 12 populations across Europe. I detected genetic differentiation among populations across Europe and locations within sampling regions for both genetic marker systems (average values: mtDNA FST = 0.574; microsatellite FST = 0.389), resulting in a lack of isolation by distance. Furthermore, several microsatellite alleles and one haplotype were shared across populations. Partitioning of molecular variance was inconsistant for both marker systems. Microsatellite variation was higher within than among populations, whereas mtDNA data yielded an inverse pattern. Relative high levels of nuclear DNA diversity were found across Europe. The amount of mitochondrial diversity was low in Spain, Hungary and Denmark. Gene flow analysis at a European scale did not reveal typical pattern of population recolonization in the light of postglacial colonization hypotheses. Populations, which recently experienced an expansion or population-bottleneck were observed both in middle and northern Europe. Since these populations revealed high genetic diversity in both marker systems, I suggest these areas to represent postglacial zones of secondary contact among divergent lineages of D. galeata. In order to reveal the relationship between population genetic structure of D. galeata and the relative contribution of environmental factors, I used a statistical framework based on canonical correspondence analysis. Although I detected no single ecological gradient mediating the genetic differentiation in either lake regions, it is noteworthy that the same ecological factors were significantly correlated with intra- and interspecific genetic variation of D. galeata. For example, I found a relationship between genetic variation of D. galeata and differentiation with higher and lower trophic levels (phytoplankton, submerged macrophytes and fish) and a relationship between clonal variation and species diversity within Cladocera. Variance partitioning had only a minor contribution of each environmental category (abiotic, biomass/density and diversity) to genetic diversity of D. galeata, while the largest proportion of variation was explained by shared components. My work illustrates the important role of ecological differentiation and adaptation in structuring genetic variation, and it highlights the need for approaches incorporating a landscape context for population divergence.
Four species of true crocodile (genus Crocodylus) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions—Crocodylus intermedius in South America, C. moreletii along the Caribbean coast of Mesoamerica, and C. rhombifer confined to Cuba. The fourth, C. acutus, is narrowly sympatric with each of the other three species. In this study, we sampled 113 crocodiles across Crocodylus populations in Cuba, as well as exemplar populations in Belize and Florida (USA), and sequenced three regions of the mitochondrial genome (D-loop, cytochrome b, cytochrome oxidase I; 3,626 base pair long dataset) that overlapped with published data previously collected from Colombia, Jamaica, and the Cayman Islands. Phylogenetic analyses of these data revealed two, paraphyletic lineages of C. acutus. One lineage, found in the continental Americas, is the sister taxon to C. intermedius, while the Greater Antillean lineage is most closely related to C. rhombifer. In addition to the paraphyly of the two C. acutus lineages, we recovered a 5.4% estimate of Tamura-Nei genetic divergence between the Antillean and continental clades. The reconstructed paraphyly, distinct phylogenetic affinities and high genetic divergence between Antillean and continental C. acutus populations are consistent with interspecific differentiation within the genus and suggest that the current taxon recognized as C. acutus is more likely a complex of cryptic species warranting a reassessment of current taxonomy. Moreover, the inclusion, for the first time, of samples from the western population of the American crocodile in Cuba revealed evidence for continental mtDNA haplotypes in the Antilles, suggesting this area may constitute a transition zone between distinct lineages of C. acutus. Further study using nuclear character data is warranted to more fully characterize this cryptic diversity, resolve taxonomic uncertainty, and inform conservation planning in this system.
Background: Mitochondrial genes are among the most commonly used markers in studies of species’ phylogeography and to draw conclusions about taxonomy. The Hyles euphorbiae complex (HEC) comprises six distinct mitochondrial lineages in the Mediterranean region, of which one exhibits a cryptic disjunct distribution. The predominant mitochondrial lineage in most of Europe, euphorbiae, is also present on Malta; however, it is nowadays strangely absent from Southern Italy and Sicily, where it is replaced by 'italica'. A separate biological entity in Italy is further corroborated by larval colour patterns with a congruent, confined suture zone along the Northern Apennines. By means of historic DNA extracted from museum specimens, we aimed to investigate the evolution of the mitochondrial demographic structure of the HEC in Italy and Malta throughout the Twentieth Century.
Results: At the beginning of the Twentieth Century, the European mainland lineages were also present at a moderate frequency in Southern Italy and Sicily. The proportion of 'italica' then steadily increased in this area from below 60 percent to near fixation in about 120 years. Thus, geographical sorting of mitochondrial lineages in the HEC was not as complete then as the current demography suggests. The pattern of an integral 'italica' core region and a disjunct euphorbiae distribution evolved very recently. To explain these strong demographic changes, we propose genetic drift due to anthropogenic habitat loss and fragmentation in combination with an impact from recent climate warming that favoured the spreading of the potentially better adapted 'italica' populations.
Conclusions: The pattern of geographically separated mitochondrial lineages is commonly interpreted as representing long term separated entities. However, our results indicate that such a pattern can emerge surprisingly quickly, even in a widespread and rather common taxon. We thus caution against drawing hasty taxonomic conclusions from biogeographical patterns of mitochondrial markers derived from modern sampling alone.
Background: The current taxonomy of the African giraffe (Giraffa camelopardalis) is primarily based on pelage pattern and geographic distribution, and nine subspecies are currently recognized. Although genetic studies have been conducted, their resolution is low, mainly due to limited sampling. Detailed knowledge about the genetic variation and phylogeography of the South African giraffe (G. c. giraffa) and the Angolan giraffe (G. c. angolensis) is lacking. We investigate genetic variation among giraffe matrilines by increased sampling, with a focus on giraffe key areas in southern Africa.
Results: The 1,562 nucleotides long mitochondrial DNA dataset (cytochrome b and partial control region) comprises 138 parsimony informative sites among 161 giraffe individuals from eight populations. We additionally included two okapis as an outgroup. The analyses of the maternally inherited sequences reveal a deep divergence between northern and southern giraffe populations in Africa, and a general pattern of distinct matrilineal clades corresponding to their geographic distribution. Divergence time estimates among giraffe populations place the deepest splits at several hundred thousand years ago.
Conclusions: Our increased sampling in southern Africa suggests that the distribution ranges of the Angolan and South African giraffe need to be redefined. Knowledge about the phylogeography and genetic variation of these two maternal lineages is crucial for the development of appropriate management strategies.
Nach der Wiederentdeckung der Mendelschen Regeln Anfang des 20. Jahrhunderts waren es unter anderem Theodosius Dobzhansky und Ernst Mayr, die Evolution erstmals durch die Analyse von Populationen untersuchten. Bis 1980 wurden für diese populationsgenetischen Analysen morphologische, cytologische und enzymelektrophoretische Marker verwendet. Durch die Entdeckung der PCR wurde das Arbeiten mit DNA wesentlich erleichtert. Im Laufe der Zeit setzte sich der Begriff Molekulare Ökologie durch, mit dem man jenen Bereich beschreiben will, der molekulare Methoden der Populationsgenetik und der Genomanalyse mit ökologischen Fragestellungen verbindet. Genetische Marker können vergangene als auch zur Zeit ablaufende Prozesse aufzeigen. Mit Hilfe solcher Marker kann man einerseits Hinweise auf die Refugialgebiete von Organismen während der letzten Eiszeiten erhalten, anderseits Prozesse wie Genfluß, Selektion oder genetische Drift aufzeigen. Bei den meisten der von uns im Folgenden vorgestellten Arbeiten steht das Sequenzieren mitochondrialer Abschnitte im Vordergrund. Die mitochondriale DNA hat durch ihre im Vergleich zu nuklearer DNA erhöhte Mutationsrate und vereinfachte Genstruktur den Vorteil, bei intraspezifischen Fragestellungen gute Resultate zu erzielen.
The identity of Barbus capensis, as described by Andrew Smith (1841), is reviewed following a careful examination of the lectotype in the Natural History Museum, London. Evidence shows clearly that it represents a specimen of the Berg-Breede River whitefish or ‘witvis’ and not the species known as the Clanwilliam yellowfish, to which it was attributed until recently. The original illustration of the species is shown to be a composite of these two different species. A replacement name for the Clanwilliam yellowfish is drawn from the earliest described synonym, Labeobarbus seeberi (Gilchrist & Thompson, 1913). Following widespread recognition that the genus Barbus Daudin, 1805 does not occur in sub-Saharan Africa, the generic status of the Berg-Breede River whitefish (witvis) and other tetraploid cyprinines of southern Africa is reviewed, taking genetic and morphological characters into account. Five distinct lineages, each representing a genus, are recognized, including the genera Pseudobarbus Smith, 1841 and Cheilobarbus Smith, 1841, and three new genera described herein: Amatolacypris gen. nov., Sedercypris gen. nov. and Namaquacypris gen. nov.
During a survey of the fishes in the region of the Wonga-Wongué Presidential Reserve, 14 new populations of the subgenus Chromaphyosemion Myers, 1924 were found. These observations extend the previously known distribution range of the subgenus 120 kilometres southward. None of these populations could be related to any described species. Based on the colouration of the males and females, together with a genetic marker (mitochondrial DNA cytochrome b sequences), the populations studied are grouped into six new species which are described in this article, all close to Aphyosemion alpha Huber, 1998 with which they share the presence of a black alpha-shaped mark on the pre- and post-opercular region. The group composed of A. alpha and the six new species is referred to here as the A. alpha species group. All the new species, A. aurantiacum Chirio, Legros & Agnèse sp. nov., A. barakoniense Chirio, Legros & Agnèse sp. nov., A. flammulatum Chirio, Legros & Agnèse sp. nov., A. flavocyaneum Chirio, Legros & Agnèse sp. nov., A. pusillum Chirio, Legros & Agnèse sp. nov. and A. rubrogaster Chirio, Legros & Agnèse sp. nov., are further unambiguously diagnosed by unique combinations of colour patterns, making it possible to generate an identification key for the A. alpha species group. It is likely that the coastal dunes of Wonga-Wongué that form a sandy relief, could have led to the fragmentation and then isolation of the hydrographical networks that flow into the Atlantic Ocean, making possible a significant number of allopatric speciations.
Phylogenetic analyses of the highly diverse (non-marine aquatic) gastropod family Hydrobiidae Stimpson, 1865 have revealed seven main lineages, most of which represent subfamilies. The subfamily Pseudamnicolinae Radoman, 1977, and specifically the genus Pseudamnicola Paulucci, 1878 (mainly inhabiting western and central Mediterranean regions), contributes substantially to this hydrobiid richness. Most of its congeners have been described in terms of their shell and penis features, which are of limited diagnostic value. Hence, the taxonomic status of some Pseudamnicola species needs to be revised, particularly of those inhabiting marginal regions, such as the Ponto-Caspian domain, largely occupied by the subfamily Pyrgulinae Brusina, 1882. Here we present a molecular phylogeny including species of both subfamilies along with extended morphological descriptions to confirm assignments of the Iranian species Pseudamnicola zagrosensis Glöer & Pešić, 2009; Sarkia kermanshahensis Glöer & Pešić, 2009 (originally within Pseudamnicola) and P. saboori Glöer & Pešić, 2009. Our COI-based tree rejects these assignments suggesting a new potential lineage, sister to the pyrgulinid species, and comprising three genera: Shadinia Akramowski, 1976, Intermaria gen. nov. and Persipyrgula gen. nov. These genera differ molecularly by 3.6%–8.5%, and are diagnosable by penis, female genitalia and radula features. Our findings evidence the high morphological variability of pyrgulinid species and provide insight into the origins and evolution of the freshwater Ponto-Caspian fauna.