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The present study aimed at assessing genetic purity of black wildebeest (Connochoetes gnou) at Abe Bailey Nature Reserve, Gauteng Province, South Africa, using a multitocus microsatellite approach. Five loci were studied in black and blue (C. taurinus) wildebeest, the latter being a closely related species and known to produce hybrids with the morphologically very similar black wildebeest. In fact, the entire national black wildebeest population of South Africa potentially contains a significant proportion of introgressed blue wildebeest genes. In our case, eight out of 39 alleles were unique to black and 22 to blue wildebeest, with nine alleles shared between pure populations of the two species in Line with their taxonomic proximity. A possible Limited past introgression of blue wildebeest genes into the Abe Bailey population, corresponding to documents on population history, was only supported by the presence of a single allele otherwise exclusively found in samples of four pure blue but not in samples of two pure black wildebeest control populations. However, an assignment test and coefficients of population divergence did not support an extended introgression of C. taurinus alleles into the C. gnou population under study. Average heterozygosity at Abe Bailey proved to be intermediate between black and blue wildebeest, the tatter species generally harbouring more genetic variation than the former owing to larger population sizes and the absence of population bottlenecks in historical times. The implications of our data are discussed with reference to the persistence of introgressed genes and the conservation of pure black wildebeest gene pools
To unravel the postglacial colonization history and the current intercolony dispersal in the common eider, Somateria mollissima, we analysed genetic variation at a part of the mitochondrial control region and five unlinked autosomal microsatellite loci in 175 eiders from 11 breeding colonies, covering the entire European distribution range of this species. As a result of extreme female philopatry, mitochondrial DNA differentiation is substantial both among local colonies and among distant geographical regions. Our study further corroborates the previous hypothesis of a single Pleistocene refugium for European eiders. A nested clade analysis on mitochondrial haplotypes suggests that (i) the Baltic Sea eider population is genetically closest to a presumably ancestral population and that (ii) the postglacial recolonization progressed in a stepwise fashion via the North Sea region and the Faroe Islands to Iceland. Current long-distance dispersal is limited. Differentiation among colonies is much less pronounced at microsatellite loci. The geographical pattern of this nuclear genetic variation is to a large extent explained by isolation by distance. As female dispersal is very limited, the geographical pattern of nuclear variation is probably explained by male-mediated gene flow among breeding colonies. Our study provides genetic evidence for the assumed prominent postglacial colonization route shaping the present terrestrial fauna of the North Atlantic islands Iceland and the Faroes. It suggests that this colonization had been a stepwise process originating in continental Europe. It is the first molecular study on eider duck populations covering their entire European distribution range
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.
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.
Using molecular genetic methods and an ancient DNA approach, we studied population and species succession of rotifers of the genus Brachionus in the Kenyan alkaline-saline crater lake Sonachi since the beginning of the 19th century as well as distribution of Brachionus haplotypes in recent and historic sediments of other lakes of the East African Rift System. The sediment core record of Lake Sonachi displays haplotypes of a distinct evolutionary lineage in all increments. Populations were dominated by a single mitochondrial haplotype for a period of 150 years, and two putatively intraspecific turnovers in dominance occurred. Both changes are concordant with major environmental perturbations documented by a profound visible change in sediment composition of the core. The first change was very abrupt and occurred after the deposition of volcanic ash at the beginning of the 19th century. The second change coincides with a major lake level lowstand during the 1940s. It was preceded by a period of successively declining lake level, in which two other haplotypes appeared in the lake. One of these putatively belongs to another species documented in historical and recent Kenyan lake sediments. The analysis of plankton population dynamics through historical time can reveal patterns of population persistence and turnover in relation to environmental changes.
It is well established that reproductive isolation often arises from genome incompatibilities and that genes encoding reproductive traits are less prone to introgression. Hybrid zones of Mytilus trossulus and Mytilus edulis provide an intriguing model to assess reproductive isolation. Although gene flow is restricted in North America, introgression is pervasive in the Baltic. This study aimed at analyzing the shape of multilocus clines across the Baltic contact zone between M. edulis and M. trossulus to infer mechanisms of restriction to gene flow. We use maximum likelihood methods to construct the best fitting individual clines for five markers located on biparentally inherited autosomes and paternally and maternally inherited mitochondrial DNA (mtDNA). Strong cline shape differences among markers suggest that reproductive isolation arising from genome-wide incompatibilities is weak, and that these discrepancies possibly result from genetic drift, hybrid zone movement or marker-specific selection. However, the finding of a common cline center for M7 lysin (involved in fertilization) and paternally transmitted mtDNA (causing nuclear-mitochondrial incompatibilities in hybrids) suggest that these loci may play a role in incomplete reproductive isolation.
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.
The meadow grasshopper, Chorthippus parallelus (Zetterstedt), is common and widespread in Central Europe, with a low dispersal range per generation. A population study in Central Germany (Frankenwald and Thuringer Schiefergebirge) showed strong interpopulation differences in abundance and individual fitness. We examined genetic variability using microsatellite markers within and between 22 populations in a short-to long-distance sampling (19 populations, Frankenwald, Schiefergebirge, as well as a southern transect), and in the Erzgebirge region (three populations), with the latter aiming to check for effects as a result of historical forest cover. Of the 671 C. parallelus captured, none was macropterous (functionally winged). All populations showed a high level of expected and observed heterozygosity (mean 0.80-0.90 and 0.60-0.75, respectively), whereas there was evidence of inbreeding (F(IS) values all positive). Allelic richness for all locus-population combinations was high (mean 9.3-11.2), whereas alleles per locus ranged from 15-62. At a local level, genic and genotypic differences were significant. Pairwise F(ST) values were in the range 0.00-0.04, indicating little interpopulation genetic differentiation. Similarly, the calculated gene flow was very high, based on the respective F(ST) (19.5) and using private alleles (7.7). A Neighbour-joining tree using Nei's D(A) and principal coordinate analysis separated two populations that were collected in the Erzgebirge region. Populations from this region may have escaped the effects of the historical forest cover. The visualization of the spatial arrangement of genotypes revealed one geographical barrier to gene flow in the short-distance sampling.
Lake Naivasha, Kenya, is one of a number of freshwater lakes in the East African Rift System. Since the beginning of the twentieth century, it has experienced greater anthropogenic influence as a result of increasingly intensive farming of coffee, tea, flowers, and other horticultural crops within its catchment. The water-level history of Lake Naivasha over the past 200 years was derived from a combination of instrumental records and sediment data. In this study, we analysed diatoms in a lake sediment core to infer past lacustrine conductivity and total phosphorus concentrations. We also measured total nitrogen and carbon concentrations in the sediments. Core chronology was established by (210)Pb dating and covered a similar to 186-year history of natural (climatic) and human-induced environmental changes. Three stratigraphic zones in the core were identified using diatom assemblages. There was a change from littoral/epiphytic diatoms such as Gomphonema gracile and Cymbella muelleri, which occurred during a prolonged dry period from ca. 1820 to 1896 AD, through a transition period, to the present planktonic Aulacoseira sp. that favors nutrient-rich waters. This marked change in the diatom assemblage was caused by climate change, and later a strong anthropogenic overprint on the lake system. Increases in sediment accumulation rates since 1928, from 0.01 to 0.08 g cm(-2) year(-1) correlate with an increase in diatom-inferred total phosphorus concentrations since the beginning of the twentieth century. The increase in phosphorus accumulation suggests increasing eutrophication of freshwater Lake Naivasha. This study identified two major periods in the lake's history: (1) the period from 1820 to 1950 AD, during which the lake was affected mainly by natural climate variations, and (2) the period since 1950, during which the effects of anthropogenic activity overprinted those of natural climate variation.
Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.
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.
Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approximately 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based denaturing high-performance liquid chromatography (DHPLC). An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length and if the amplicons differed only in a small number of nucleotides. Generally, the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.
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.
The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymor-phisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.
Background
Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats.
Results
The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats.
Conclusions
Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become – at least locally – extinct.
The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor.
The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany
(2019)
The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany.