Refine
Has Fulltext
- no (12)
Year of publication
Document Type
- Article (12) (remove)
Language
- English (12)
Is part of the Bibliography
- yes (12) (remove)
Keywords
- Bucerotidae (2)
- Microsatellites (2)
- microsatellites (2)
- Aceros (1)
- Arabidopsis thaliana (1)
- Biogeography (1)
- Conservation genetics (1)
- Cross-species amplification (1)
- Cuora (1)
- Cytochrome b (1)
- Divergent evolution (1)
- Fresh water fish (1)
- Genetic diversity loss (1)
- Intraspecific genetic variation (1)
- Island biogeography (1)
- Mediterranean temporary ponds (1)
- Mitochondrial control region I (1)
- Penelopides Philippine hornbills (1)
- Philippine archipelago (1)
- Phylogeny (1)
- Phylogeography (1)
- Positive selection (1)
- SSRs (1)
- Somateria mollissima (1)
- Starch metabolizing enzymes (1)
- Testudines (1)
- Transcript levels (1)
- box turtles (1)
- captive breeding (1)
- conservation units (1)
- diaptomid copepods (1)
- eider duck (1)
- indirect fitness (1)
- intraspecific brood parasitism (1)
- relatedness (1)
Institute
Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
Objective
The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean.
Results
For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade.
Spotlight on islands
(2018)
Groups of proximate continental islands may conceal more tangled phylogeographic patterns than oceanic archipelagos as a consequence of repeated sea level changes, which allow populations to experience gene flow during periods of low sea level stands and isolation by vicariant mechanisms during periods of high sea level stands. Here, we describe for the first time an ancient and diverging lineage of the Italian wall lizard Podarcis siculus from the western Pontine Islands. We used nuclear and mitochondrial DNA sequences of 156 individuals with the aim of unraveling their phylogenetic position, while microsatellite loci were used to test several a priori insular biogeographic models of migration with empirical data. Our results suggest that the western Pontine populations colonized the islands early during their Pliocene volcanic formation, while populations from the eastern Pontine Islands seem to have been introduced recently. The inter-island genetic makeup indicates an important role of historical migration, probably due to glacial land bridges connecting islands followed by a recent vicariant mechanism of isolation. Moreover, the most supported migration model predicted higher gene flow among islands which are geographically arranged in parallel. Considering the threatened status of small insular endemic populations, we suggest this new evolutionarily independent unit be given priority in conservation efforts.
Hemidiaptomus diaptomid copepods are known to be excellent biological indicators for the highly biodiverse crustacean communities inhabiting Mediterranean temporary ponds (MTPs), an endangered inland water habitat whose conservation is considered a priority according to the "Habitat Directive" of the European Union. This study reports on the characterization of five polymorphic microsatellite loci in Hemidiaptomus gurneyi, to be used as markers for fine-scale studies on the population genetic structure and metapopulation dynamics of a typical and obligate MTP dweller. The five selected loci proved to be polymorphic in the species, with three to five polymorphic loci per studied population. Overall, mean heterozygosity scored for all loci and populations was lower than that reported for the few other diaptomid species for which microsatellite loci have been to date described; this is possibly due to the intrinsically fragmented and isolated peculiar habitat inhabited by the species. Furthermore, the presence of indels within the flanking regions of selected loci was scored. This study, albeit confirming the technical difficulties in finding proper microsatellite markers in copepods, provides for the first time a set of useful polymorphic microsatellite loci for a Hemidiaptomus species, thus allowing the realization of fine-scale phylogeographic and population genetics studies of this flagship crustacean taxon for MTPs.
Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.
We isolated and characterized 16 new di- and tetranudeotide microsatellite markers for the critically endangered Asian box turtle genus Cuora, focusing on the "Cuora trifasciata" species complex. The new markers were then used to analyse genetic variability and divergence amongst five described species within this complex, namely C. aurocapitata (n = 18), C. cyclornata (n = 31), C. pani (n = 6), C. trifasciata (n = 58), and C. zhoui (n = 7). Our results support the view that all five species represent valid taxa. Within two species (C. trifasciata and C. cyclornata), two distinct morphotypes were corroborated by microsatellite divergence. For three individuals, morphologically identified as being of hybrid origin, the hybrid status was confirmed by our genetic analysis. Our results confirm the controversial species (Cuora aurocapitata, C. cyclornata) and subspecies/morphotypes (C. cyclornata meieri, C. trifasciata cf. trifasciata) to be genetically distinct, which has critical implications for conservation strategies.
Intraspecific brood parasitism (IBP) is a remarkable phenomenon by which parasitic females can increase their reproductive output by laying eggs in conspecific females' nests in addition to incubating eggs in their own nest. Kin selection could explain the tolerance, or even the selective advantage, of IBP, but different models of IBP based on game theory yield contradicting predictions. Our analyses of seven polymorphic autosomal microsatellites in two eider duck colonies indicate that relatedness between host and parasitizing females is significantly higher than the background relatedness within the colony. This result is unlikely to be a by-product of relatives nesting in close vicinity, as nest distance and genetic identity are not correlated. For eider females that had been ring-marked during the decades prior to our study, our analyses indicate that (i) the average age of parasitized females is higher than the age of nonparasitized females, (ii) the percentage of nests with alien eggs increases with the age of nesting females, (iii) the level of IBP increases with the host females' age, and (iv) the number of own eggs in the nest of parasitized females significantly decreases with age. IBP may allow those older females unable to produce as many eggs as they can incubate to gain indirect fitness without impairing their direct fitness: genetically related females specialize in their energy allocation, with young females producing more eggs than they can incubate and entrusting these to their older relatives. Intraspecific brood parasitism in ducks may constitute cooperation among generations of closely related females.