Molecular Ecology
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Deciphering life history transcriptomes in different environments Abstract We compared whole transcriptome variation in six pre‐adult stages and seven adult female ages in two populations of cactophilic Drosophila mojavensis reared on two host plants to understand how differences in gene expression influence standing life history variation. We used singular value decomposition (SVD ) to identify dominant trajectories of life cycle gene expression variation, performed pairwise comparisons of stage and age differences in gene expression across the life cycle, identified when genes exhibited maximum levels of life cycle gene expression, and assessed population and host cactus effects on gene expression. Life cycle SVD analysis returned four significant components of transcriptional variation, revealing functional enrichment of genes responsible for growth, metabolic function, sensory perception, neural function, translation and ageing. Host cactus effects on female gene expression revealed population‐ and stage‐specific differences, including significant host plant effects on larval metabolism and development, as well as adult neurotransmitter binding and courtship behaviour gene expression levels. In 3‐ to 6‐day‐old virgin females, significant upregulation of genes associated with meiosis and oogenesis was accompanied by downregulation of genes associated with somatic maintenance, evidence for a life history trade‐off. The transcriptome of D. mojavensis reared in natural environments throughout its life cycle revealed core developmental transitions and genome‐wide influences on life history variation in natural populations.
Molecular Ecology - Tập 24 Số 1 - Trang 151-179 - 2015
Nuclear DNA‐based markers for plant evolutionary biology While DNA‐based markers can provide a wealth of information for the study of plant evolutionary biology, progress is limited by the lack of primers available for PCR. To overcome this limitation, we outline a protocol for developing oligonucleotide primers targeting regions of low copy‐number nuclear genes. This protocol is intended to lead to universally useful primer sets. To test our approach, we designed eight primer sets and tested their abilities to amplify targets from representatives of each dicot and one monocot subclass. Five of the eight primer sets amplified targets from at least five of the seven taxa and thus exhibited broad taxonomic usefulness; the remaining primers were rather specific, however, and amplified targets from at most three taxa. In only one primer‐taxon combination was a complex multiple‐banded amplification produced. Overall, the protocol outlined proved quite useful at identifying broadly applicable primers targeted to low copy‐number nuclear genes. Wider application of this approach should be effective at greatly increasing the amount of genetic information available for a diversity of plant nuclear genomes.
Molecular Ecology - Tập 6 Số 2 - Trang 113-118 - 1997
Diversity of algal endosymbionts (zooxanthellae) in octocorals: the roles of geography and host relationships Abstract The presence, genetic identity and diversity of algal endosymbionts (Symbiodinium ) in 114 species from 69 genera (20 families) of octocorals from the Great Barrier Reef (GBR), the far eastern Pacific (EP) and the Caribbean was examined, and patterns of the octocoral–algal symbiosis were compared with patterns in the host phylogeny. Genetic analyses of the zooxanthellae were based on ribosomal DNA internal transcribed spacer 1 (ITS1) region. In the GBR samples, Symbiodinium clades A and G were encountered with A and G being rare. Clade B zooxanthellae have been previously reported from a GBR octocoral, but are also rare in octocorals from this region. Symbiodinium G has so far only been found in Foraminifera, but is rare in these organisms. In the Caribbean samples, only Symbiodinium clades B and C are present. Hence, Symbiodinium diversity at the level of phylogenetic clades is lower in octocorals from the Caribbean compared to those from the GBR. However, an unprecedented level of ITS1 diversity was observed within individual colonies of some Caribbean gorgonians, implying either that these simultaneously harbour multiple strains of clade B zooxanthellae, or that ITS1 heterogeneity exists within the genomes of some zooxanthellae. Intracladal diversity based on ITS should therefore be interpreted with caution, especially in cases where no independent evidence exists to support distinctiveness, such as ecological distribution or physiological characteristics. All samples from EP are azooxanthellate. Three unrelated GBR taxa that are described in the literature as azooxanthellate (Junceella fragilis , Euplexaura nuttingi and Stereonephthya sp. 1) contain clade G zooxanthellae, and their symbiotic association with zooxanthellae was confirmed by histology. These corals are pale in colour, whereas related azooxanthellate species are brightly coloured. The evolutionary loss or gain of zooxanthellae may have altered the light sensitivity of the host tissues, requiring the animals to adopt or reduce pigmentation. Finally, we superimposed patterns of the octocoral–algal symbiosis onto a molecular phylogeny of the host. The data show that many losses/gains of endosymbiosis have occurred during the evolution of octocorals. The ancestral state (azooxanthellate or zooxanthellate) in octocorals remains unclear, but the data suggest that on an evolutionary timescale octocorals can switch more easily between mixotrophy and heterotrophy compared to scleractinian corals, which coincides with a low reliance on photosynthetic carbon gain in the former group of organisms.
Molecular Ecology - Tập 14 Số 8 - Trang 2403-2417 - 2005
Internal transcribed spacer repeat‐specific primers and the analysis of hybridization in the <i>Glycine tomentella</i> (Leguminosae) polyploid complex Abstract Polyploid and diploid hybridization is a ubiquitous and evolutionarily important phenomenon in the plant world. Determining the parental species of a hybrid, however, is difficult. Molecular markers such as the nuclear ribosomal DNA gene complex, particularly its internal transcribed spacer (ITS) region, have proved powerful in determining hybrid parentage. In some cases, population and genomic phenomena, such as genetic drift and concerted evolution, result in the loss of all or many of the tandemly repeated copies derived from one parental species, making the recovery of hybrid history difficult or impossible. Methods such as direct sequencing and cloning are typically used to find ITS sequences contributed from parental species, but are limited in their ability to detect rare repeat types. Here we report that repeat‐specific polymerase chain reaction primers can recover rare parental ITS sequences in the Glycine tomentella polyploid complex. In three allopolyploid lineages of this complex, repeat‐specific primers reliably detected rare repeats that both direct sequencing and the screening of many cloned sequences failed to detect. Other strategies, such as the use of exclusion primers, may detect rare parental repeat types in hybrids when previous hypotheses regarding the second parental species are lacking.
Molecular Ecology - Tập 11 Số 12 - Trang 2691-2702 - 2002
Nuclear ribosomal DNA (nrDNA) concerted evolution in natural and artificial hybrids of <i>Armeria</i> (Plumbaginaceae) Abstract Nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences from artificial hybrids and backcrosses between Armeria villosa ssp. longiaristata and A. colorata were studied to assess the possible effects of concerted evolution in natural hybrids. F1 artificial hybrids show the expected pattern of additive polymorphisms for five of the six variable sites as estimated from direct sequences. However, homogenization of polymorphism is already observed in the F2 , and is biased towards A. colorata except for one site. In backcrosses, an expected tendency towards homogenization of polymorphic sites in the direction of the recurrent parent is observed for five sites, although this does not necessarily imply concerted evolution. Conversely, the sixth site appears to elude such a mechanism and thus provides additional support for the occurrence of biased concerted evolution. Our findings are relevant to interpreting phylogeographic patterns involving gene flow and are also consistent with the hypothesis of a hybrid origin of A. villosa ssp. carratracensis .
Molecular Ecology - Tập 8 Số 8 - Trang 1341-1346 - 1999
The public world of insect vibrational communication
Molecular Ecology - Tập 20 Số 10 - Trang 2041-2043 - 2011
Temporal changes in kin structure through a population cycle in a territorial bird, the red grouse <i>Lagopus lagopus scoticus</i> Abstract Populations of red grouse (Lagopus lagopus scoticus ) undergo regular multiannual cycles in abundance. The ‘kinship hypothesis’ posits that such cycles are caused by changes in kin structure among territorial males producing delayed density‐dependent changes in aggressiveness, which in turn influence recruitment and regulate density. The kinship hypothesis makes several specific predictions about the levels of kinship, aggressiveness and recruitment through a population cycle: (i) kin structure will build up during the increase phase of a cycle, but break down prior to peak density; (ii) kin structure influences aggressiveness, such that there will be a negative relationship between kinship and aggressiveness over the years; (iii) as aggressiveness regulates recruitment and density, there will be a negative relationship between aggressiveness in one year and both recruitment and density in the next; (iv) as kin structure influences recruitment via an affect on aggressiveness, there will be a positive relationship between kinship in one year and recruitment the next. Here we test these predictions through the course of an 8‐year cycle in a natural population of red grouse in northeast Scotland, using microsatellite DNA markers to resolve changing patterns of kin structure, and supra‐orbital comb height of grouse as an index of aggressiveness. Both kin structure and aggressiveness were dynamic through the course of the cycle, and changing patterns were entirely consistent with the expectations of the kinship hypothesis. Results are discussed in relation to potential drivers of population regulation and implications of dynamic kin structure for population genetics.
Molecular Ecology - Tập 17 Số 10 - Trang 2544-2551 - 2008
Phylogeography of Asian wild rice, <i>Oryza rufipogon</i>: a genome‐wide view Abstract Asian wild rice (Oryza rufipogon ) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa ). Studies of the geographic structure of O. rufipogon , based on chloroplast and low‐copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon . However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome‐wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome‐wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova , we conclude that there are two genetically distinct O. rufipogon groups, Ruf‐I and Ruf‐II. The two groups exhibit a clinal variation pattern generally from north‐east to south‐west. Different from many earlier studies, Ruf‐I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica , whereas Ruf‐II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica , is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration–drift balance in creating this clinal variation pattern is also discussed.
Molecular Ecology - Tập 21 Số 18 - Trang 4593-4604 - 2012
Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake Abstract The fate of antibiotic resistance genes (ARG s) in environmental microbial communities is of primary concern as prodromal of a potential transfer to pathogenic bacteria. Although of diverse origin, the persistence of ARG s in aquatic environments is highly influenced by anthropic activities, allowing potential control actions in well‐studied environments. However, knowledge of abundance and space–time distribution of ARG s in ecosystems is still scarce. Using quantitative real‐time PCR, we investigated the presence and the abundance of twelve ARG s (against tetracyclines, β‐lactams, aminoglycosides, quinolones and sulphonamides) at different sampling sites, depths and seasons, in Lake Maggiore, a large subalpine lake, and in the area of its watershed. We then evaluated the correlation between each ARG and a number of ecological parameters in the water column in the deepest part of the lake. Our results suggest the constitutive presence of at least four ARG s within the bacterial community with a high proportion of bacteria potentially resistant to tetracyclines and sulphonamides. The presence of these ARG s was independent of the total bacterial density and temperature. The dynamics of tet (A) and sulII ARG s and the factors allowing their persistence in waters.
Molecular Ecology - Tập 24 Số 15 - Trang 3888-3900 - 2015
Host dispersal shapes the population structure of a tick‐borne bacterial pathogen Abstract Birds are hosts for several zoonotic pathogens. Because of their high mobility, especially of longdistance migrants, birds can disperse these pathogens, affecting their distribution and phylogeography. We focused onBorrelia burgdorferi sensu lato, which includes the causative agents of Lyme borreliosis, as an example for tick‐borne pathogens, to address the role of birds as propagation hosts of zoonotic agents at a large geographical scale. We collected ticks from passerine birds in 11 European countries.B . burgdorferi s.l. prevalence inIxodes spp. was 37% and increased with latitude. The fieldfareTurdus pilaris and the blackbirdT. merula carried ticks with the highestBorrelia prevalence (92 and 58%, respectively), whereas robinErithacus rubecula ticks were the least infected (3.8%).Borrelia garinii was the most prevalent genospecies (61%), followed byB. valaisiana (24%),B. afzelii (9%),B. turdi (5%) andB. lusitaniae (0.5%). A novelBorrelia genospecies “Candidatus Borrelia aligera” was also detected. Multilocus sequence typing (MLST ) analysis ofB. garinii isolates together with the global collection ofB. garinii genotypes obtained from theBorrelia MLST public database revealed that: (a) there was little overlap among genotypes from different continents, (b) there was no geographical structuring within Europe, and (c) there was no evident association pattern detectable amongB. garinii genotypes from ticks feeding on birds, questing ticks or human isolates. These findings strengthen the hypothesis that the population structure and evolutionary biology of tick‐borne pathogens are shaped by their host associations and the movement patterns of these hosts.
Molecular Ecology - Tập 29 Số 3 - Trang 485-501 - 2020
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