Papers by Darina Koubínová
Plants, Mar 4, 2024
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Academy of Sciences, Czech Republic/Ústav biologie obratlovců Akademie věd České republiky) Koubí... more Academy of Sciences, Czech Republic/Ústav biologie obratlovců Akademie věd České republiky) Koubínová, D, 2013. Phylogeny of selected African bat species based on the cytogenetic and molecular approaches. Ph.D. Thesis.
Zoology in The Middle East, 2010
Plants, Apr 20, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Evolutionary Ecology, Nov 28, 2014
Scientific Reports, Oct 23, 2017
Biotic interactions are often acknowledged as catalysers of genetic divergence and eventual expla... more Biotic interactions are often acknowledged as catalysers of genetic divergence and eventual explanation of processes driving species richness. We address the question, whether extreme ecological specialization is always associated with lineage sorting, by analysing polymorphisms in morphologically similar ecotypes of the myrmecophilous butterfly Maculinea alcon. The ecotypes occur in either hygric or xeric habitats, use different larval host plants and ant species, but no significant distinctive molecular traits have been revealed so far. We apply genome-wide RAD-sequencing to specimens originating from both habitats across Europe in order to get a view of the potential evolutionary processes at work. Our results confirm that genetic variation is mainly structured geographically but not ecologicallyspecimens from close localities are more related to each other than populations of each ecotype from distant localities. However, we found two loci for which the association with xeric versus hygric habitats is supported by segregating alleles, suggesting convergent evolution of habitat preference. Thus, ecological divergence between the forms probably does not represent an early stage of speciation, but may result from independent recurring adaptations involving few genes. We discuss the implications of these results for conservation and suggest preserving biotic interactions and main genetic clusters. Biotic interactions represent essential components of ecosystems 1. Ecological relationships such as host-parasite, resource-consumer, mutualism or competition, affect the realized ecological niche of species and, consequently, their reaction to habitat changes 2,3. The impact of such changes should be higher in ecological specialists, rather than generalists, as specialists are usually more constrained by their specific biotic and abiotic requirements 4. Strong interactions and more specific needs may thus lead to faster isolation of populations and development of reproductive barriers. The evolution of different ecotypes may be associated with genetic differentiation, catalyzing lineage divergence and eventually driving the speciation processes 5-8. Shifts in host-plant associations are found in many herbivorous insects, such as butterflies, in which it is often considered one of the main mechanisms producing their observed diversity 9-11. However, in order to drive differential selection, the host-plant association character (most importantly adaptation to its defense secondary metabolites) should be inherited, variable, and conferring a local advantage. Whether or not host-plant association shifts occurred repeatedly within a species' populations, or are associated with a deeper divergence of
Acta Chiropterologica, Dec 1, 2010
According to current phylogenetic hypotheses, the bats of the families Rhinolophidae and Hipposid... more According to current phylogenetic hypotheses, the bats of the families Rhinolophidae and Hipposideridae are sister groups nested within the clade of Pteropodiformes. A conservative nature of karyotypic evolution was previously reported within the two families. Karyotypes with diploid number (2n) varying between 58 and 62 chromosomes were assumed to prevail among the rhinolophid species, whereas, karyotypes with 32 chromosomes were found in most of the hipposiderid bats. However, divergent lower or higher 2n numbers have been recorded in some species in both families. Variation is documented in the present paper by examination of non-differentially stained karyotypes in 10 species belonging to genera Rhinolophus and Hipposideros from western Africa and southern India. Among the species studied, the karyotypes with a 2n of 32, 36, 52, 56, 58, and 62, and with relatively stable number of autosomal arms (FNa = 60, 62, 64) were recorded.
Parasitology Research, Sep 14, 2015
Sedentary bird species are suitable model hosts for identifying potential vectors of avian blood ... more Sedentary bird species are suitable model hosts for identifying potential vectors of avian blood parasites. We studied haemosporidian infections in the Tengmalm's Owl (Aegolius funereus) in the Ore Mountains of the Czech Republic using molecular detection methods. Sex of owl nestlings was scored using molecular sexing based on fragment analysis of PCR-amplified CHD1 introns. Observed infection prevalences in nestlings and adult owls were 51 and 86 %, respectively. Five parasite lineages were detected. Most of the infections comprised the Leucocytozoon AEFUN02 and STOCC06 lineages that probably refer to distinct Leucocytozoon species. Other lineages were detected only sporadically. Mixed infections were found in 49 % of samples. The main factor affecting the probability of infection was host age. No effect of individual sex on infection probability was evidenced. The youngest infected nestling was 12 days old. High parasite prevalence in the Tengmalm's Owl nestlings suggests that insect vectors must enter nest boxes to transmit parasites before fledging. Hence, we placed sticky insect traps into modified nest boxes, collected potential insect vectors, and examined them for the presence of haemosporidian parasites using molecular detection. We trapped 201 insects which were determined as biting midges from the Culicoides genus and two black fly species, Simulium (Nevermannia) vernum and Simulium (Eusimulium) angustipes. Six haemosporidian lineages were detected in the potential insect vectors, among which the Leucocytozoon lineage BT2 was common to the Tengmalm's Owl and the trapped insects. However, we have not detected the most frequently encountered Tengmalm's Owl Leucocytozoon lineages AEFUN02 and STOCC06 in insects.
Molecular Phylogenetics and Evolution, Jul 1, 2021
Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resol... more Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short Tandem Repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples from Capurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. Altogether, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.
Frontiers in Plant Science, Jul 12, 2019
Phylogenomics of Neotropical Geonomateae Palms a large genomic dataset is provided for an entire ... more Phylogenomics of Neotropical Geonomateae Palms a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro-and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.
Katedra zoologieDepartment of ZoologyFaculty of SciencePřírodovědecká fakult
Univerzita Karlova, Přírodovědecká fakulta, Sep 18, 2007
Folia Zoologica -Praha-
Conventional and G-banded karyotypes are reported for three species of molossid bats from india (... more Conventional and G-banded karyotypes are reported for three species of molossid bats from india (Chaerephon plicatus) and Senegal (Ch. pumilus, Mops condylurus). The chromosome diploid number 2n = 48 and the number of chromosomal arms FN= 54 were recorded, similarly as in the previous published reports on karyology of molossid bats from Thailand, East Malaysia, and Africa. A synopsis of karyotypes of bats of the family Molossidae is presented with comments on their chromosomal evolution.
Frontiers in Zoology, 2013
Introduction: The Vespertilionidae is the largest family of bats, characterized by high occurrenc... more Introduction: The Vespertilionidae is the largest family of bats, characterized by high occurrence of morphologically convergent groups, which impedes the study of their evolutionary history. The situation is even more complicated in the tropics, where certain regions remain under-sampled. Results: Two hundred and thirteen vespertilionid bats from Senegal (West Africa) were studied with the use of non-differentially stained karyotypes and multi-locus sequence data analysed with maximum likelihood and Bayesian methods. These bats were identified as 10 different taxa, five of which were distinctive from their nominate species (Pipistrellus hesperidus, Nycticeinops schlieffenii, Scotoecus hirundo, Neoromicia nana and N. somalica), based on both karyotypes and molecular data. These five cryptic taxa are unrelated, suggesting that these West African populations have long been isolated from other African regions. Additionally, we phylogenetically analysed 166 vespertilionid taxa from localities worldwide using GenBank data (some 80% of the genera of the family) and 14 representatives of closely related groups, together with our Senegalese specimens. The systematic position of several taxa differed from previous studies and the tribes Pipistrellini and Vespertilionini were redefined. The African Pipistrellus rueppellii was basal to the Pipistrellus/Nyctalus clade and the Oriental species Glischropus tylopus was basal to the East Asian pipistrelles within the tribe Pipistrellini. The African genus Neoromicia was confirmed to be diphyletic. Based on GenBank data, Eptesicus was polyphyletic, with the Asian E. nasutus and E. dimissus both supported as phylogenetically distinct from the Eptesicus clade. The subfamily Scotophilinae was confirmed as one of the basal branches of Vespertilionidae. Conclusions: New taxa and new systematic arrangements show that there is still much to resolve in the vespertilionids and that West Africa is a biogeographic hotspot with more diversity to be discovered.
Plants
The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial–interglacial ... more The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial–interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting fr...
Molecular Ecology, 2022
The importance of hybridization and introgression is well documented in the evolution of plants, ... more The importance of hybridization and introgression is well documented in the evolution of plants, however, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using the ddRADseq protocol, we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer likely occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes.
ddRADseq data aligned. The first number of the labels indicates the mitochondrial lineage
Alignment of Wolbachia fragments found in the ddRADseq data
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Papers by Darina Koubínová