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Molecular Phylogenetics and Evolution 04/2013; 67(1):300-1. · 3.61 Impact Factor
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ABSTRACT: Geological processes and ecological adaptation are major drivers of diversification on oceanic islands. Although diversification in these islands is often interpreted as resulting from dispersal or island hopping rather than vicariance, this may not be the case in islands with complex geological histories. The island of Tenerife, in the Canary Islands, emerged in the late Miocene as 3 precursor islands that were subsequently connected and reisolated by volcanic cycles. The spider Dysdera verneaui is endemic to the island of Tenerife, where it is widely distributed throughout most island habitats, providing an excellent model to investigate the role of physical barriers and ecological adaptation in shaping within-island diversity. Here, we present evidence that the phylogeographic patterns of this species trace back to the independent emergence of the protoislands. Molecular markers (mitochondrial genes cox1, 16S, and nad1 and the nuclear genes ITS-2 and 28S) analyzed from 100 specimens (including a thorough sampling of D. verneaui populations and additional outgroups) identify 2 distinct evolutionary lineages that correspond to 2 precursor islands, each with diagnostic genital characters indicative of separate species status. Episodic introgression events between these 2 main evolutionary lineages explain the observed incongruence between mitochondrial and nuclear markers, probably as a result of the homogenization of their ITS-2 sequence types. The most widespread lineage exhibits a complex population structure, which is compatible with either secondary contact, following connection of deeply divergent lineages, or alternatively, a back colonization from 1 precursor island to another.
The Journal of heredity 03/2013; · 2.05 Impact Factor
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ABSTRACT: Because of female-biased illegal harvesting, knowledge about the genetic mating system of the black spiny-tailed iguana Ctenosaura pectinata is of primary interest for the conservation of this threatened species. Based on the high levels of multiple paternity found
in clutches of many other reptiles, particularly in lizards, it is hypothesised that multiple paternity may also be common
in black iguanas. This was investigated by using microsatellite DNA to estimate the number of males siring nine litters (9
mothers, 121 offspring genotyped at ten polymorphic loci) of black iguanas. Contrary to expectations, only 11% of sampled
black iguana females produced litters consistent with being sired by multiple males. These data are the first evidence for
the predominance of single paternity within an iguanid lizard, and suggest that black iguana may be more susceptible to loss
of genetic variation in the face of gender-biased over-hunting pressure than previously thought.
Keywords
Ctenosaura pectinata
-Microsatellites-Genetic monogamy-Reptile-Mexico
Conservation Genetics 04/2012; 11(5):1645-1652. · 1.61 Impact Factor
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ABSTRACT: In northwestern Iberia, two largely allopatric Lacerta lepida mitochondrial lineages occur, L5 occurring to the south of Douro River and L3 to the north, with a zone of putative secondary contact in the region of the Douro River valley. Cytochrome b sequence chromatograms with polymorphisms at nucleotide sites diagnostic for the two lineages were detected in individuals in the region of the Douro River and further north within the range of L3. We show that these polymorphisms are caused by the presence of four different numts (I-IV) co-occurring with the L3 genome, together with low levels of heteroplasmy. Two of the numts (I and II) are similar to the mitochondrial genome of L5 but are quite divergent from the mitochondrial genome of L3 where they occur. We show that these numts are derived from the mitochondrial genome of L5 and were incorporated in L3 through hybridization at the time of secondary contact between the lineages. The additional incidence of these numts to the north of the putative contact zone is consistent with an earlier postglacial northward range expansion of L5, preceding that of L3. We show that genetic exchange between the lineages responsible for the origin of these numts in L3 after secondary contact occurred prior to, or coincident with, the northward expansion of L3. This study shows that, in the context of phylogeographic analysis, numts can provide evidence for past demographic events and can be useful tools for the reconstruction of complex evolutionary histories.
Molecular Ecology 02/2012; 21(4):1005-18. · 5.52 Impact Factor
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ABSTRACT: Population bottlenecks can restrict variation at functional genes, reducing the ability of populations to adapt to new and changing environments. Understanding how populations generate adaptive genetic variation following bottlenecks is therefore central to evolutionary biology. Genes of the major histocompatibility complex (MHC) are ideal models for studying adaptive genetic variation due to their central role in pathogen recognition. While de novo MHC sequence variation is generated by point mutation, gene conversion can generate new haplotypes by transferring sections of DNA within and across duplicated MHC loci. However, the extent to which gene conversion generates new MHC haplotypes in wild populations is poorly understood. We developed a 454 sequencing protocol to screen MHC class I exon 3 variation across all 13 island populations of Berthelot's pipit (Anthus berthelotii). We reveal that just 11-15 MHC haplotypes were retained when the Berthelot's pipit dispersed across its island range in the North Atlantic ca. 75,000 years ago. Since then, at least 26 new haplotypes have been generated in situ across populations. We show that most of these haplotypes were generated by gene conversion across divergent lineages, and that the rate of gene conversion exceeded that of point mutation by an order of magnitude. Gene conversion resulted in significantly more changes at nucleotide sites directly involved with pathogen recognition, indicating selection for functional variants. We suggest that the creation of new variants by gene conversion is the predominant mechanism generating MHC variation in genetically depauperate populations, thus allowing them to respond to pathogenic challenges.
Molecular Ecology 11/2011; 20(24):5213-25. · 5.52 Impact Factor
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ABSTRACT: A combined morphological, molecular and biological study shows that the weevil species presently named Mecinus janthinus is actually composed of two different cryptic species: M. janthinus Germar, 1821 and M. janthiniformis Toševski & Caldara sp.n. These species are morphologically distinguishable from each other by a few very subtle morphological characters. On the contrary, they are more readily distinguishable by both molecular and biological characters. A molecular assessment based on the mitochondrial DNA cytochrome oxidase subunit II gene revealed fixed differences between the two species with p-distances between samples of both species ranging from 1.3 to 2.4%. In addition to this, the larvae of the two species are found to develop on different species within the genus Linaria (Plantaginaceae): M. janthinus is associated with yellow toadflax (L. vulgaris) and M. janthiniformis with broomleaf toadflax (L. genistifolia) and Dalmatian toadflax (L. dalmatica). Molecular and host use records further suggest the occurrence of a third species associated with L. vulgaris within M. janthinus, sampled from north Switzerland, central Hungary and east Serbia. The significance of these new findings is of particular importance because species of the M. janthinus group are used, or are potential candidates, for the biological control of invasive toadflaxes in North America.
Systematic Entomology 09/2011; 36(4):741 - 753. · 2.94 Impact Factor
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ABSTRACT: The widespread phenomenon of polyandry (mating by females with multiple males) is an evolutionary puzzle, because females can sustain costs from promiscuity, whereas full fertility can be provided by a single male. Using the red flour beetle, Tribolium castaneum, we identify major fitness benefits of polyandry to females under inbreeding, when the risks of fertilization by incompatible male haplotypes are especially high. Fifteen generations after inbred populations had passed through genetic bottlenecks, we recorded increased levels of female promiscuity compared with noninbred controls, most likely due to selection from prospective fitness gains through polyandry. These data illustrate how this common mating pattern can evolve if population genetic bottlenecks increase the risks of fitness depression due to fertilization by sperm carrying genetically incompatible haplotypes.
Science 09/2011; 333(6050):1739-42. · 31.20 Impact Factor
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ABSTRACT: There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages.
Philosophical Transactions of The Royal Society B Biological Sciences 08/2011; 366(1576):2391-402. · 6.40 Impact Factor
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ABSTRACT: Aim To delimit the distribution of matrilines of the black iguana (Ctenosaura pectinata), detect potential contact zones between them, and test the hypothesis of geographic concordance in the structuring of matrilines with respect to genetic structuring across the nuclear genome.Location Pacific coast of Mexico in the states of Nayarit, Jalisco, Colima, Michoacán in the lowlands adjacent to the western end of the Mexican Volcanic Belt.Methods Tissue samples were obtained every 10–20 km along a transect across the range of three previously described mitochondrial DNA (mtDNA) clades of C. pectinata. Iguanas were genotyped with 11 nuclear microsatellites and maternal lineages were inferred based on mtDNA sequences. Geographic structure and geographic concordance between biparentally and maternally inherited markers were analysed with clustering methods, FST and NST indexes as well as haplotype networks.Results Geographic structure was evident for both markers and the existence of contact zones confirmed. Nevertheless, the distribution of nuclear and mtDNA genetic variation is not geographically concordant. Four matrilines exist in the area, whereas only two nuclear clusters occur. A contact zone between nuclear clusters extends along a distance of c. 60 km, and introgression is evident in individuals from several localities.Main conclusions High levels of genetic diversity were detected on the western coast of Mexico. Historical and contemporaneous processes seem to shape the distribution of genetic variation in C. pectinata. There are no evident geographic, environmental or ecological barriers that coincide with genetic subdivisions, and the observed mtDNA structure is likely to be the result of past climatic changes. The less structured distribution of nuclear genetic variation is consistent with the homogenizing effect of male-biased dispersal. Our findings have implications for the taxonomy and conservation strategies for this threatened species, and highlight the fact that geographic analyses of both cytoplasmic and nuclear genetic variation are important for the meaningful inference of evolutionary and demographic histories.
Journal of Biogeography 06/2011; 38(7):1394 - 1405. · 4.54 Impact Factor
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ABSTRACT: The Iberian Peninsula is recognized as an important refugial area for species survival and diversification during the climatic cycles of the Quaternary. Recent phylogeographic studies have revealed Iberia as a complex of multiple refugia. However, most of these studies have focused either on species with narrow distributions within the region or species groups that, although widely distributed, generally have a genetic structure that relates to pre-Quaternary cladogenetic events. In this study we undertake a detailed phylogeographic analysis of the lizard species, Lacerta lepida, whose distribution encompasses the entire Iberian Peninsula. We attempt to identify refugial areas, recolonization routes, zones of secondary contact and date demographic events within this species.
Results support the existence of 6 evolutionary lineages (phylogroups) with a strong association between genetic variation and geography, suggesting a history of allopatric divergence in different refugia. Diversification within phylogroups is concordant with the onset of the Pleistocene climatic oscillations. The southern regions of several phylogroups show a high incidence of ancestral alleles in contrast with high incidence of recently derived alleles in northern regions. All phylogroups show signs of recent demographic and spatial expansions. We have further identified several zones of secondary contact, with divergent mitochondrial haplotypes occurring in narrow zones of sympatry.
The concordant patterns of spatial and demographic expansions detected within phylogroups, together with the high incidence of ancestral haplotypes in southern regions of several phylogroups, suggests a pattern of contraction of populations into southern refugia during adverse climatic conditions from which subsequent northern expansions occurred. This study supports the emergent pattern of multiple refugia within Iberia but adds to it by identifying a pattern of refugia coincident with the southern distribution limits of individual evolutionary lineages. These areas are important in terms of long-term species persistence and therefore important areas for conservation.
BMC Evolutionary Biology 06/2011; 11:170. · 3.52 Impact Factor
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ABSTRACT: Closely related species that show clear phenotypic divergence, but without obvious geographic barriers, can provide opportunities to study how diversification can occur when opportunities for allopatric speciation are limited. We examined genetic divergence in the coral reef fish genus Hypoplectrus (family: Serranidae), which comprises of 10-14 morphotypes that are distinguished solely by their distinct colour patterns, but which show little genetic differentiation. Our goal was to detect loci that show clear disequilibrium between morphotypes and across geographical locations. We conducted Amplified Fragment Length Polymorphism molecular analysis to quantify genetic differentiation among, and selection between, morphotypes. Three loci were consistently divergent beyond neutral expectations in repeated pair-wise morphotype comparisons using two different methods. These loci provide the first evidence for genes that may be associated with colour morphotype in the genus Hypoplectrus.
PLoS ONE 01/2011; 6(6):e20394. · 4.09 Impact Factor
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ABSTRACT: As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle Tribolium castaneum impacts on male reproductive fitness in the absence or presence of male-male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P(2) 'offence' role in sperm competition was significantly more depressed under inbreeding than sperm 'defence' (P(1)). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated.
Proceedings of the Royal Society B: Biological Sciences 11/2010; 277(1699):3483-91. · 5.41 Impact Factor
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ABSTRACT: Between-individual variance in potential reproductive rate theoretically creates a load in reproducing populations by driving sexual selection of male traits for winning competitions, and female traits for resisting the costs of multiple mating. Here, using replicated experimental evolution under divergent operational sex ratios (OSR, 9:1 or 1:6 ♀:♂) we empirically identified the parallel reproductive fitness consequences for females and males in the promiscuous flour beetle Tribolium castaneum. Our results revealed clear evidence that sexual conflict resides within the T. castaneum mating system. After 20 generations of selection, females from female-biased OSRs became vulnerable to multiple mating, and showed a steep decrease in reproductive fitness with an increasing number of control males. In contrast, females from male-biased OSRs showed no change in reproductive fitness, irrespective of male numbers. The divergence in reproductive output was not explained by variation in female mortality. Parallel assays revealed that males also responded to experimental evolution: individuals from male-biased OSRs obtained 27% greater reproductive success across 7-day competition for females with a control male rival, compared to males from the female-biased lines. Subsequent assays suggest that these differences were not due to postcopulatory sperm competitiveness, but to precopulatory/copulatory competitive male mating behavior.
Evolution 11/2010; 65(3):713-24. · 5.15 Impact Factor
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ABSTRACT: The analysis of ancient DNA in a population genetic or phylogeographical framework is an emerging field, as traditional analytical tools were largely developed for the purpose of analysing data sampled from a single time point. Markov chain Monte Carlo approaches have been successfully developed for the analysis of heterochronous sequence data from closed panmictic populations. However, attributing genetic differences between temporal samples to mutational events between time points requires the consideration of other factors that may also result in genetic differentiation. Geographical effects are an obvious factor for species exhibiting geographical structuring of genetic variation. The departure from a closed panmictic model require researchers to either exploit software developed for the analysis of isochronous data, take advantage of simulation approaches using algorithms developed for heterochronous data, or explore approximate Bayesian computation. Here, we review statistical approaches employed and available software for the joint analysis of ancient and modern DNA, and where appropriate we suggest how these may be further developed.
Molecular Ecology Resources 09/2010; 10(5):760-72. · 3.06 Impact Factor
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ABSTRACT: Plant feeding insects and the plants they feed upon represent an ecological association that is thought to be a key factor for the diversification of many plant feeding insects, through differential adaptation to different plant selective pressures. While a number of studies have investigated diversification of plant feeding insects above the species level, relatively less attention has been given to patterns of diversification within species, particularly those that also require plants for oviposition and subsequent larval development. In the case of plant feeding insects that also require plant tissues for the completion of their reproductive cycle through larval development, the divergent selective pressure not only acts on adults, but on the full life history of the insect. Here we focus attention on Rhinusa antirrhini (Curculionidae), a species of weevil broadly distributed across Europe that both feeds on, and oviposits and develops within, species of the plant genus Linaria (Plantaginaceae). Using a combination of mtDNA (COII) and nuclear DNA (EF1-alpha) sequencing and copulation experiments we assess evidence for host associated genetic differentiation within R. antirrhini. We find substantial genetic variation within this species that is best explained by ecological specialisation on different host plant taxa. This genetic differentiation is most pronounced in the mtDNA marker, with patterns of genetic variation at the nuclear marker suggesting incomplete lineage sorting and/or gene flow between different host plant forms of R. antirrhini, whose origin is estimated to date to the mid-Pliocene (3.77 Mya; 2.91-4.80 Mya).
Molecular Ecology 05/2010; 19(11):2286-300. · 5.52 Impact Factor
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ABSTRACT: A molecular phylogeny of the subtribe Calathina was inferred from DNA sequence data from the mitochondrial cox1-cox2 region and the nuclear genes 28S and EF-1alpha. All lineages within Calathina from the Holarctic region were represented except for the monotypic subgenus Tachalus. Maximum Parsimony and Bayesian analyses of the combined data set showed that the subtribe is a monophyletic lineage that includes a single genus Calathus, where other taxa currently ranked as independent genera (Lindrothius, Synuchidius, Thermoscelis and Acalathus) are nested within this genus.Neocalathus and Lauricalathus, both subgenera of Calathus, were found to be polyphyletic and in need of taxonomic revision. The subtribe appears to have originated in the Mediterranean Basin and thereafter expanded into most parts of the Palearctic region, the Macaronesian archipelagos (at least five independent colonisation events), the Ethiopian highlands and the Nearctic region (at least two independent events).
Molecular Phylogenetics and Evolution 11/2009; 55(2):358-71. · 3.61 Impact Factor
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ABSTRACT: The increasing ability to extract and sequence DNA from noncontemporaneous tissue offers biologists the opportunity to analyse ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. In this study, we provide a critical assessment of Bayesian Markov chain Monte Carlo (MCMC) analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates because of model misspecification when the data come from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However, when model misspecification is only mild, then the 95% highest posterior density intervals provide adequate frequentist coverage of the true rates.
Molecular Ecology 10/2009; 18(21):4390-7. · 5.52 Impact Factor
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ABSTRACT: We isolated and characterized 10 polymorphic microsatellite loci from the Mexican black iguana (Ctenosaura pectinata) and assessed levels of polymorphism in sampling sites located in the northern areas of the species' distribution range. Two to 19 alleles per locus and observed heterozygosity ranging from 0.15 to 0.96 were detected. These markers will be useful to describe population genetic structure, the extent of gene flow in contact zones, to study the mating system of the species and to address conservation genetics issues. Additionally, we evaluated the potential utility of these markers for studies of other species within the genus Ctenosaura (i.e. C. hemilopha, C. similis and C. oaxacana).
Molecular Ecology Resources 01/2009; 9(1):117-9. · 3.06 Impact Factor
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ABSTRACT: Exotic pathogens have been implicated in the decline and extinction of various native-island-bird species. Despite the fact
that there is increasing concern about the introduction of diseases in island ecosystems, little is known about parasites
in the islands of Macaronesia. We focus on Berthelot’s pipit (Anthus berthelotii), an endemic and widespread Macaronesian bird species, using a combination of field studies and molecular techniques to determine:
(1) the range and prevalence of avian pox and malaria in Berthelot’s pipits throughout the species’ distribution, (2) the
genetic characterization of both parasites in order to ascertain the level of host specificity. We sampled 447 pipits across
the 12 islands inhabited by this species. Overall, 8% of all individuals showed evidence of pox lesions and 16% were infected
with avian malaria, respectively. We observed marked differences in the prevalence of parasites among islands both within
and between archipelagos. Avian pox prevalence varied between 0–54% within and between archipelagos and avian malaria prevalence
varied between 0–64% within and between archipelagos. The diversity of pathogens detected was low: only two genetic lineages
of avian malaria and one lineage of avian pox were found to infect the pipit throughout its range. Interestingly, both avian
malaria parasites found were Plasmodium spp. that had not been previously reported in the Macaronesian avifauna (but that had been observed in the lesser kestrel
Falco naumannii), while the avian pox was a host specific lineage that had previously been reported on two of the Canary Islands.
Parasitology Research 10/2008; 103(6):1435-1443. · 2.15 Impact Factor
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ABSTRACT: Evolutionary ecologists are increasingly combining phylogenetic data with distributional and ecological data to assess how and why communities of species differ from random expectations for evolutionary and ecological relatedness. Of particular interest have been the roles of environmental filtering and competitive interactions, or alternatively neutral effects, in dictating community composition. Our goal is to place current research within a dynamic framework, specifically using recent phylogenetic studies from insular environments to provide an explicit spatial and temporal context. We compare communities over a range of evolutionary, ecological and geographic scales that differ in the extent to which speciation and adaptation contribute to community assembly and structure. This perspective allows insights into the processes that can generate community structure, as well as the evolutionary dynamics of community assembly.
Trends in Ecology & Evolution 10/2008; 23(11):619-30. · 15.75 Impact Factor
