Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Genomics and the challenging translation into conservation practice
Shafer, A.B.A. ; Wolf, J.B.W. ; Alves, P.C. ; Bergstrom, L. ; Bruford, M.W. ; Brannstrom, I. ; Colling, G. ; Dalen, L. van; Meester, L. de; Ekblom, R. ; Vergeer, P. - \ 2015
Trends in Ecology and Evolution 30 (2015)2. - ISSN 0169-5347 - p. 78 - 87.
genetic diversity - background selection - population genomics - insular population - dna - divergence - speciation - evolution - sequence - markers
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
Neandertal Admixture in Eurasia Confirmed by Maximum-Likelihood Analysis of Three Genomes
Lohse, K. ; Frantz, L.A.F. - \ 2014
Genetics 196 (2014)4. - ISSN 0016-6731 - p. 1241 - 1251.
ancestral population sizes - dna-sequences - divergence - speciation - history - number - recombination - coalescent - migration - inference
Although there has been much interest in estimating histories of divergence and admixture from genomic data, it has proved difficult to distinguish recent admixture from long-term structure in the ancestral population. Thus, recent genome-wide analyses based on summary statistics have sparked controversy about the possibility of interbreeding between Neandertals and modern humans in Eurasia. Here we derive the probability of full mutational configurations in nonrecombining sequence blocks under both admixture and ancestral structure scenarios. Dividing the genome into short blocks gives an efficient way to compute maximum-likelihood estimates of parameters. We apply this likelihood scheme to triplets of human and Neandertal genomes and compare the relative support for a model of admixture from Neandertals into Eurasian populations after their expansion out of Africa against a history of persistent structure in their common ancestral population in Africa. Our analysis allows us to conclusively reject a model of ancestral structure in Africa and instead reveals strong support for Neandertal admixture in Eurasia at a higher rate (3.4-7.3%) than suggested previously. Using analysis and simulations we show that our inference is more powerful than previous summary statistics and robust to realistic levels of recombination.
A Story of Large Land Owners and Math Skills: Inequality and Human Capital Formation in the Long-Run Development, 1820-2000
Baten, J. ; Juif, D.T. - \ 2014
Journal of Comparative Economics 42 (2014)2. - ISSN 0147-5967 - p. 375 - 401.
factor endowments - income-distribution - economic-growth - institutions - history - divergence - geography - numeracy - outcomes - africa
We create a new dataset to test the influence of land inequality on long-run human capital formation in a global cross-country study and assess the importance of land inequality relative to income inequality. Our results show that early land inequality has a detrimental influence on math and science skills even a century later. We find that this influence is causal, using an instrumental variable (IV) approach with geological, climatic and other variables that are intrinsically exogenous. A second major contribution of our study is our assessment of the persistence of numerical cognitive skills, which are an important component of modern human capital measures. Early numeracy around 1820 is estimated using the age-heaping strategy. We argue that countries with early investments in numerical education entered a path-dependency of human capital-intensive industries, including skill-intensive agriculture and services. The combined long-run effects of land inequality and human capital path-dependence are assessed for the first time in this article.
A genetic linkage map of Sole (Solea solea): A tool for evolutionary and comparative analyses of exploited (flat)fishes
Diopere, E. ; Maes, G.E. ; Komen, J. ; Volckaert, F.A.M. ; Groenen, M. - \ 2014
PLoS ONE 9 (2014)12. - ISSN 1932-6203 - 16 p.
turbot scophthalmus-maximus - common sole - microsatellite markers - comparative genomics - marine fishes - populations - time - divergence - pleuronectiformes - senegalensis
Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L.) is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes), Nile tilapia (Oreochromis niloticus), three-spined stickleback (Gasterosteus aculeatus) and green spotted pufferfish (Tetraodon nigroviridis). This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus), another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one) a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species.
Footprints of selection in wild populations of Bicyclus anynana along a latitudinal cline
Jong, M.A. de; Collins, S. ; Beldade, P. ; Brakefield, P.M. ; Zwaan, B.J. - \ 2013
Molecular Ecology 22 (2013)2. - ISSN 0962-1083 - p. 341 - 353.
drosophila-melanogaster - eastern australia - life-history - genetic responses - stress resistance - wing pattern - evolution - polymorphism - divergence - adaptation
One of the major questions in ecology and evolutionary biology is how variation in the genome enables species to adapt to divergent environments. Here, we study footprints of thermal selection in candidate genes in six wild populations of the afrotropical butterfly Bicyclus anynana sampled along a c. 3000 km latitudinal cline. We sequenced coding regions of 31 selected genes with known functions in metabolism, pigment production, development and heat shock responses. These include genes for which we expect a priori a role in thermal adaptation and, thus, varying selection pressures along a latitudinal cline, and genes we do not expect to vary clinally and can be used as controls. We identified amino acid substitution polymorphisms in 13 genes and tested these for clinal variation by correlation analysis of allele frequencies with latitude. In addition, we used two FST-based outlier methods to identify loci with higher population differentiation than expected under neutral evolution, while accounting for potentially confounding effects of population structure and demographic history. Two metabolic enzymes of the glycolytic pathway, UGP and Treh, showed clinal variation. The same loci showed elevated population differentiation and were identified as significant outliers. We found no evidence of clines in the pigmentation genes, heat shock proteins and developmental genes. However, we identified outlier loci in more localized parts of the range in the pigmentation genes yellow and black. We discuss that the observed clinal variation and elevated population divergence in UGP and Treh may reflect adaptation to a geographic thermal gradient.
Repeated parallel evolution reveals limiting similarity in subterranean diving beetles
Vergnon, R.O.H. ; Leijs, P. ; Nes, E.H. van; Scheffer, M. - \ 2013
American Naturalist 182 (2013)1. - ISSN 0003-0147 - p. 67 - 75.
species-diversity - competition - dytiscidae - patterns - convergence - coexistence - coleoptera - divergence - morphology - community
The theory of limiting similarity predicts that co-occurring species must be sufficiently different to coexist. Although this idea is a staple of community ecology, convincing empirical evidence has been scarce. Here we examine 34 subterranean beetle communities in arid inland Australia that share the same habitat type but have evolved in complete isolation over the past 5 million years. Although these communities come from a range of phylogenetic origins, we find that they have almost invariably evolved to share a similar size structure. The relative positions of coexisting species on the body size axis were significantly more regular across communities than would be expected by chance, with a size ratio, on average, of 1.6 between coexisting species. By contrast, species' absolute body sizes varied substantially from one community to the next. This suggests that self-organized spacing according to limiting-similarity theory, as opposed to evolution toward preexisting fixed niches, shaped the communities. Using a model starting from random sets of founder species, we demonstrate that the patterns are indeed consistent with evolutionary self-organization. For less isolated habitats, the same model predicts the coexistence of multiple species in each regularly spaced functional group. Limiting similarity, therefore, may also be compatible with the coexistence of many redundant species. © 2013 by The University of Chicago.
Multi-locus phylogenies of the genus Barteria (Passifloraceae) protray complex patterns in the evolution of myrmecophytism.
Peccoud, J. ; Piatscheck, F. ; Yockteng, R. ; Garcia, M. ; Sauve, M. ; Djieto-Lordon, C. ; Harris, D.J. ; Wieringa, J.J. ; Breteler, F.J. ; Born, C. ; McKey, D. ; Blatrix, R. - \ 2013
Molecular Phylogenetics and Evolution 66 (2013)3. - ISSN 1055-7903 - p. 824 - 832.
chloroplast dna - rain-forest - population - sequences - ants - pseudomyrmecinae - euphorbiaceae - divergence - protection - mutualism
The four species of the central African genus Barteria show variation in habitat and in degree of association with ants. Whereas B. solida, restricted to submontane forests, attracts opportunistic ants to extrafloral nectar, the three other species, found in lowland rainforests (B. fistulosa, B. dewevrei) and in littoral scrub (B. nigritana), possess stem domatia of varying shapes and degrees of specialisation, hosting either non-specific arboreal ants (B. nigritana, some B. dewevrei) or two large species of ants of the genus Tetraponera Smith, 1852 that are specific to some species of Barteria (B. fistulosa, some B. dewevrei). We aimed to investigate whether this variation represents an evolutionary trend toward increasing specialisation of mutualism or the reduction or loss of myrmecophytic traits. For this, we determined phylogenetic relationships within the genus using DNA sequences (primarily nuclear ITS) and microsatellite genotypes (11 loci) on a large sample of individuals, mostly from Cameroon and Gabon. The two types of markers support an initial dichotomy that groups B. dewevrei with B. nigritana and B. fistulosa with B. solida respectively. Within these pairs, species do not appear reciprocally monophyletic. At microsatellite loci, B. nigritana forms a clade embedded within B. dewevrei; and within both B. solida and B. fistulosa, geographical populations show levels of differentiation similar to that observed between populations of B. solida and B. fistulosa. Geographic distance alone does not account for genetic differentiation between species, which indicates reproductive isolation. Divergence in each of the two pairs implies evolutionary transitions in habitat and in myrmecophytism. Specialised mutualism with specific ant species of the genus Tetraponera has been lost in species found in more marginal habitats.
A combination of functionally different plant traits provides a means to quantitatively predict a broad range of species assemblages in NW Europe
Douma, J.C. ; Aerts, R. ; Witte, J.P.M. ; Bekker, R.M. ; Kunzmann, D. ; Metselaar, K. ; Bodegom, P.M. van - \ 2012
Ecography 35 (2012)4. - ISSN 0906-7590 - p. 364 - 373.
vegetatietypen - plantenecologie - vegetation types - plant ecology - relative growth-rate - community ecology - strategies - diversity - convergence - divergence - patterns - model - components - nitrogen
Assembly theory predicts that filtering processes will select species by their attributes to build a community. Some filters increase functional similarity among species, while others lead to dissimilarity. Assuming converging processes to be dominant within habitats, we tested in this study whether species assemblages across a wide range of habitats can be distinguished quantitatively by their mean trait compositions. In addition, we investigated how many and which traits are needed to describe the differences between species assemblages best. The approach has been applied on a dataset that included 12 plant traits and 7644 vegetation releves covering a wide range of habitats in the Netherlands. We demonstrate that due to the dominant role of converging processes 1) the functional composition can explain up to 80% of the floristic differences between species assemblages using seven plant traits, showing that plant trait combinations provide a powerful tool for predicting the occurrence of species assemblages across different habitats; 2) to achieve a high performance, traits should be taken from different strategy components, i.e. traits that are functionally orthogonal, which does not necessarily coincide with low trait-trait correlations; 3) the different strategy components identified in this study correspond to the strategy components of some conventional plant ecological strategy schemes (PESS) schemes to describe the variation between individual species. However, some PESS merge traits into one strategy component that are shown to be functionally different when predicting species assemblages. If such PESS is used to predict assemblages, this leads to a loss in predictive capacity. Potentially, our new approach is globally applicable to quantify community assembly patterns. However this needs to be tested.
Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K-T boundary in Madagascar
Crottinia, A. ; Madsen, O. ; Poux, C. ; Straussa, A. ; Vieites, D.R. ; Vences, M. - \ 2012
Proceedings of the National Academy of Sciences of the United States of America 109 (2012)14. - ISSN 0027-8424 - p. 5358 - 5363.
species richness - ocean currents - dispersal - diversification - divergence - hypothesis - vicariance - phylogeny - evolution - radiation
The geographic and temporal origins of Madagascar's biota have long been in the center of debate. We reconstructed a time-tree including nearly all native nonflying and nonmarine vertebrate clades present on the island, from DNA sequences of two single-copy protein-coding nuclear genes (BDNF and RAG1) and a set of congruent time constraints. Reconstructions calculated with autocorrelated or independent substitution rates over clades agreed in placing the origins of the 31 included clades in Cretaceous to Cenozoic times. The two clades with sister groups in South America were the oldest, followed by those of a putative Asian ancestry that were significantly older than the prevalent clades of African ancestry. No colonizations from Asia occurred after the Eocene, suggesting that dispersal and vicariance of Asian/Indian groups were favored over a comparatively short period during, and shortly after, the separation of India and Madagascar. Species richness of clades correlates with their age but those clades that have a large proportion of species diversity in rainforests are significantly more species-rich. This finding suggests an underlying pattern of continuous speciation through time in Madagascar's vertebrates, with accelerated episodes of adaptive diversification in those clades that succeeded radiating into the rainforests.
The Development of a Genome Wide SNP Set for the Barnacle Goose Branta leucopsis
Jonker, R.M. ; Zhang, Q. ; Hooft, W.F. van; Loonen, M.J.J.E. ; Jeugd, H.P. van der; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Prins, H.H.T. ; Kraus, Robert - \ 2012
PLoS ONE 7 (2012)7. - ISSN 1932-6203
breeding range expansion - migratory connectivity - bird migration - geese - markers - conservation - relatedness - populations - divergence - evolution
Migratory birds are of particular interest for population genetics because of the high connectivity between habitats and populations. A high degree of connectivity requires using many genetic markers to achieve the required statistical power, and a genome wide SNP set can fit this purpose. Here we present the development of a genome wide SNP set for the Barnacle Goose Branta leucopsis, a model species for the study of bird migration. We used the genome of a different waterfowl species, Mallard Anas platyrhynchos, as a reference to align Barnacle Goose second generation sequence reads from an RRL library and detected 2188 SNPs genome wide. Furthermore, we used chimeric flanking sequences, merged from both Mallard and Barnacle Goose DNA sequence information, to create primers for validation by genotyping. Validation with a 384 SNP genotyping set resulted in 374 (97%) successfully typed SNPs in the assay, of which 358 (96%) were polymorphic. Additionally, we validated our SNPs on relatively old (30 years) museum samples, which resulted in a success rate of at least 80%. This shows that museum samples could be used in standard SNP genotyping assays. Our study also shows that the genome of a related species can be used as reference to detect genome wide SNPs in birds, because genomes of birds are highly conserved. This is illustrated by the use of chimeric flanking sequences, which showed that the incorporation of flanking nucleotides from Mallard into Barnacle Goose sequences lead to equal genotyping performance when compared to flanking sequences solely composed of Barnacle Goose sequence
Landscape prerequisites for the survival of a modelled metapopulation and its neutral genetic diversity are affected by climate change
Cobben, M.M.P. ; Verboom, J. ; Opdam, P.F.M. ; Hoekstra, R.F. ; Jochem, R. ; Smulders, M.J.M. - \ 2012
Landscape Ecology 27 (2012). - ISSN 0921-2973 - p. 227 - 237.
klimaatverandering - metapopulaties - kolonisatie - modellen - climatic change - metapopulations - colonization - models - frog rana-arvalis - population - biodiversity - differentiation - implementation - connectivity - adaptation - divergence - migration - responses
In response to climate change a species may move, adapt, or go extinct. For the adaptability of a population its genetic diversity is essential, but climate change-induced range shifts can cause a loss of genetic diversity. We investigated how landscape structure affects the level and distribution of genetic diversity in metapopulations subject to climate change-induced range shifts. For this we used the spatially explicit, individual-based model METAPHOR which simulates metapopulation demography and genetics under different temperature increase scenarios. The results indicated that increasing total habitat area may enhance the maintenance of the genetic diversity in metapopulations while they are shifting their range under climate change. However, the results also showed that a high level of total habitat area did not prevent the populations in the newly colonised habitat area of being depleted of much of the original genetic diversity. We therefore conclude that enhancing landscape connectivity may lead to a delayed loss of genetic diversity in metapopulations under climate change, but that additional measures would be necessary to ensure its long-term conservation. Importantly, our simulations also show that a landscape which could be regarded as well-structured under stable climatic conditions, may be inferior for the conservation of genetic diversity during a range shift. This is important information for landscape management when developing strategies for the in situ conservation of genetic variation in natural populations under climate change.
Overshooting dynamics in a model adaptive radiation
Meyer, J.R. ; Schoustra, S.E. ; LaChapelle, J. ; Kassen, R.K. - \ 2011
Proceedings of the Royal Society. B: Biological Sciences 278 (2011). - ISSN 0962-8452 - p. 392 - 398.
pseudomonas-fluorescens - experimental evolution - experimental populations - diversification - divergence - diversity - phenotype - history
The history of life is punctuated by repeated periods of unusually rapid evolutionary diversification called adaptive radiation. The dynamics of diversity during a radiation reflect an overshooting pattern with an initial phase of exponential-like increase followed by a slower decline. Much attention has been paid to the factors that drive the increase phase, but far less is known about the causes of the decline phase. Decreases in diversity are rarely associated with climatic changes or catastrophic events, suggesting that they may be an intrinsic consequence of diversification. We experimentally identify the factors responsible for losses in diversity during the later stages of the model adaptive radiation of the bacterium Pseudomonas fluorescens. Proximately, diversity declines because of the loss of biofilm-forming niche specialist morphotypes. We show that this loss occurs despite the presence of strong divergent selection late in the radiation and is associated with continued adaptation of resident niche specialists to both the biotic and abiotic environments. These results suggest that losses of diversity in the latter stages of an adaptive radiation may be a general consequence of diversification through competition and lends support to the idea that the conditions favouring the emergence of diversity are different from those that ensure its long-term maintenance
Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos)
Kraus, R.H.S. ; Kersten, H.H.D. ; Hooft, W.F. van; Crooijmans, R.P.M.A. ; Poel, J.J. van der; Elmberg, J. ; Vignal, A. ; Huang, Y. ; Li, N. ; Prins, H.H.T. ; Groenen, M.A.M. - \ 2011
BMC Genomics 12 (2011). - ISSN 1471-2164 - 11 p.
pathogenic avian influenza - conservation - divergence - markers - virus - birds - power - base - map
Background - Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. Results - More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. Conclusion We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.
An Atlas of Type I MADS Box Gene Expression during Female Gametophyte and Seed Development in Arabidopsis[W].
Bemer, M. ; Heijmans, K. ; Airoldi, C.A. ; Davies, B. ; Angenent, G.C. - \ 2010
Plant Physiology 154 (2010)1. - ISSN 0032-0889 - p. 287 - 300.
genome-wide identification - polycomb group gene - endosperm development - central cell - egg cell - fertilization - protein - family - transformation - divergence
Members of the plant type I MADS domain subfamily have been reported to be involved in reproductive development in Arabidopsis (Arabidopsis thaliana). However, from the 61 type I genes in the Arabidopsis genome, only PHERES1, AGAMOUS-LIKE80 (AGL80), DIANA, AGL62, and AGL23 have been functionally characterized, which revealed important roles for these genes during female gametophyte and early seed development. The functions of the other genes are still unknown, despite the fact that the available single T-DNA insertion mutants have been largely investigated. The lack of mutant phenotypes is likely due to a considerable number of recent intrachromosomal duplications in the type I subfamily, resulting in nonfunctional genes in addition to a high level of redundancy. To enable a breakthrough in type I MADS box gene characterization, a framework needs to be established that allows the prediction of the functionality and redundancy of the type I genes. Here, we present a complete atlas of their expression patterns during female gametophyte and seed development in Arabidopsis, deduced from reporter lines containing translational fusions of the genes to green fluorescent protein and ß-glucuronidase. All the expressed genes were revealed to be active in the female gametophyte or developing seed, indicating that the entire type I subfamily is involved in reproductive development in Arabidopsis. Interestingly, expression was predominantly observed in the central cell, antipodal cells, and chalazal endosperm. The combination of our expression results with phylogenetic and protein interaction data allows a better identification of putative redundantly acting genes and provides a useful tool for the functional characterization of the type I MADS box genes in Arabidopsis
Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis
Skinner, M. ; Robertson, L.B. ; Tempest, H.G. ; Langley, E.J. ; Ioannou, D. ; Fowler, K.E. ; Crooijmans, R.P.M.A. - \ 2009
BMC Genomics 10 (2009). - ISSN 1471-2164 - 11 p.
copy number variation - anas-platyrhynchos - segmental duplications - gallus-domesticus - avian genome - evolution - chromosomes - conservation - divergence - genes
Background: The availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey (Meleagris gallopavo) and the first analysis of copy number variants (CNVs) in birds. Here, we extend this approach to the Pekin duck (Anas platyrhynchos), an obvious target for comparative genomic studies due to its agricultural importance and resistance to avian flu. Results: We provide a detailed molecular cytogenetic map of the duck genome through FISH assignment of 155 chicken clones. We identified one inter- and six intrachromosomal rearrangements between chicken and duck macrochromosomes and demonstrated conserved synteny among all microchromosomes analysed. Array comparative genomic hybridisation revealed 32 CNVs, of which 5 overlap previously designated "hotspot" regions between chicken and turkey. Conclusion: Our results suggest extensive conservation of avian genomes across 90 million years of evolution in both macro- and microchromosomes. The data on CNVs between chicken and duck extends previous analyses in chicken and turkey and supports the hypotheses that avian genomes contain fewer CNVs than mammalian genomes and that genomes of evolutionarily distant species share regions of copy number variation ("CNV hotspots"). Our results will expedite duck genomics, assist marker development and highlight areas of interest for future evolutionary and functional studies
Allopatric origin of cryptic butterfly species that were discovered feeding on distinct host plants in sympatry.
McBride, L.C. ; Velzen, R. van; Larsen, T.B. - \ 2009
Molecular Ecology 18 (2009)17. - ISSN 0962-1083 - p. 3639 - 3651.
parasitoid flies diptera - dna barcodes - mitochondrial-dna - reproductive isolation - astraptes-fulgerator - phytophagous insects - speciation - evolution - lepidoptera - divergence
Surveys of tropical insects are increasingly uncovering cryptic species ¿ morphologically similar yet reproductively isolated taxa once thought to comprise a single interbreeding entity. The vast majority of such species are described from a single location. This leaves us with little information on geographic range and intraspecific variation and limits our ability to infer the forces responsible for generating such diversity. For example, in herbivorous and parasitic insects, multiple specialists are often discovered within what were thought to be single more generalized species. Host shifts are likely to have contributed to speciation in these cases. But when and where did those shifts occur, and were they facilitated by geographic isolation? We attempted to answer these questions for two cryptic species within the butterfly Cymothoe egesta that were recently discovered on different host plants in central Cameroon. We first used mtDNA markers to separate individuals collected on the two hosts within Cameroon and then extended our analysis to incorporate individuals collected across the entire pan-Afrotropical range of the original taxon. To our surprise, we found that the species are almost entirely allopatric, dividing the original range and overlapping only in the narrow zone of West-Central Africa where they were first discovered in sympatry. This finding, combined with analyses of genetic variation within each butterfly species, strongly suggests that speciation occurred in allopatry, probably during the Pleistocene. We discuss the implications of our results for understanding speciation among other cryptic species recently discovered in the tropics and argue that more work is needed on geographic patterns and host usage in such taxa
The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits
Schoch, C.L. ; Sung, G.H. ; López-Giráldez, F. ; Townsend, J.P. ; Miadlikowska, J. ; Hofstetter, V. ; Robbertse, B. ; Brandon Matheny, P. ; Kauff, F. ; Wang, Z. ; Gueidan, C. ; Andrie, R.M. ; Trippe, K. ; Ciufetti, L.M. ; Wynns, A. ; Fraker, E. ; Hodkinson, B.P. ; Bonito, G. ; Groenewald, J.Z. ; Arzanlou, M. ; Hoog, G.S. de; Crous, P.W. ; Hewitt, D. ; Pfister, D.H. ; Peterson, K. ; Gryzenhout, M. ; Wingfield, M.J. ; Aptroot, A. ; Suh, S.O. ; Blackwell, M. ; Hillis, D.M. ; Griffith, G.W. ; Castlebury, L.A. ; Rossman, A.Y. ; Lumbsch, H.T. ; Lücking, R. ; Büdel, B. ; Rauhut, A. ; Diederich, P. ; Ertz, D. ; Geiser, D.M. ; Hosaka, K. ; Inderbitzin, P. ; Kohlmeyer, J. ; Volkmann-Kohlmeyer, B. ; Mostert, L. ; O'Donnell, K. ; Sipman, H. ; Rogers, J.D. ; Shoemaker, R.A. ; Sugiyama, J. ; Summerbell, R.C. ; Untereiner, W. ; Johnston, P.R. ; Stenroos, S. ; Zuccaro, A. ; Dyer, P.S. ; Crittenden, P.D. ; Cole, M.S. ; Hansen, K. ; Trappe, J.M. ; Yahr, R. ; Lutzoni, F. ; Spatafora, J.W. - \ 2009
Systematic Biology 58 (2009)2. - ISSN 1063-5157 - p. 224 - 239.
rna-polymerase-ii - multiple sequence alignment - fungal lineages - cleistothecial fungi - classification - subunit - pezizomycotina - divergence - morphology - eukaryotes
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
The LEDA Traitbase: a database of life-history traits of the Northwest European flora
Kleyer, M. ; Bekker, R.M. ; Knevel, I.C. ; Bakker, J.P. ; Thompson, K. ; Sonnenschein, M. ; Poschlod, P. ; Groenendael, J.M. van; Klimes, L. ; Klimesova, J. ; Klotz, S. ; Rusch, G.M. ; Hermy, M. ; Adriaens, D. ; Boedeltje, G. ; Bossuyt, B. ; Dannemann, A. ; Endels, P. ; Götzenberger, L. ; Hodgson, J.G. ; Jackel, A.K. ; Kühn, L. ; Kunzmann, D. ; Ozinga, W.A. ; Römermann, C. ; Stadler, M. ; Schlegelmilch, J. ; Steendam, H.J. ; Tackenberg, O. ; Wilmann, B. ; Cornelissen, J.H.C. ; Eriksson, O. ; Garnier, E. ; Peco, B. - \ 2008
Journal of Ecology 96 (2008). - ISSN 0022-0477 - p. 1266 - 1274.
plant functional traits - trade-off - communities - dispersal - mechanisms - consequences - regeneration - biodiversity - divergence - attributes
An international group of scientists has built an open internet data base of life-history traits of the Northwest European flora (the LEDA-Traitbase) that can be used as a data source for fundamental research on plant biodiversity and coexistence, macro-ecological patterns and plant functional responses. The species-trait matrix comprises referenced information under the control of an editorial board, for ca. 3000 species of the Northwest European flora, combining existing information and additional measurements. The data base currently contains data on 26 plant traits that describe three key features of plant dynamics: persistence, regeneration and dispersal. The LEDA-Traitbase is freely available at http://www.leda-traitbase.org. We present the structure of the data base and an overview of the trait information available. Synthesis. The LEDA Traitbase is useful for large-scale analyses of functional responses of communities to environmental change, effects of community trait composition on ecosystem properties and patterns of rarity and invasiveness, as well as linkages between traits as expressions of fundamental trade-offs in plants.
Institutions, reform policies and productivity growth in agriculture: evidence from former communist countries
Rizov, M.I. - \ 2008
NJAS Wageningen Journal of Life Sciences 55 (2008)4. - ISSN 1573-5214 - p. 307 - 323.
overgangslandbouw - verandering - centraal-europa - collectieve landbouwbedrijven - staatslandbouwbedrijven - particuliere landbouwbedrijven - transitional farming - change - central europe - collective farms - state farms - private farms - initial conditions - eastern-europe - land-reform - panel-data - transition economies - common heritage - soviet-union - performance - divergence - efficiency
There are important differences among former communist countries in performance of their agricultural sectors that are commonly attributed to variation in inherent institutions and reform policy choices. In this paper the link between institutions, reforms and (labour) productivity growth in agriculture is analysed within an augmented neo-classical growth model framework derived from a production function. For the empirical analysis panel data over the transition period (1990-2001) were used that cover 15 former communist countries, applying a GMM-IV estimator. Estimation results strongly support the view that the shift to individual land use, measuring farm restructuring, as well as the overall economic reforms, supported by democratic institutions, have positively contributed to the (labour) productivity growth in former communist countries¿ agriculture.
Lacustrine spawning: is this a new reproductive strategy among 'large' African cyprinid fishes?
Graaf, M. de; Nentwich, E.D. ; Osse, J.W.M. ; Sibbing, F.A. - \ 2005
Journal of Fish Biology 66 (2005)5. - ISSN 0022-1112 - p. 1214 - 1236.
barbus-intermedius complex - lake tana ethiopia - species flock - adaptive radiation - speciation - evolution - divergence - salmon - diversification - segregation
Changes in the gonadosomatic index and abundance of the different Labeobarbus species in the mouths of four major afferent rivers of Lake Tana, Ethiopia, were monitored monthly during 1999 and 2000. Riverine spawning was characteristic for seven of Lake Tana's 15 contemporary Labeobarbus species. These seven did not show spatial segregation among afferent rivers but significant temporal segregation occurred in aggregating in the river mouths and migrating towards the upstream spawning areas during the breeding season (June¿October). Among the eight other species, peak gonad development occurred generally in the same period as in the riverine spawners. These species, however, did not aggregate in the river mouths during the breeding period and were absent from the upstream spawning areas. A derived, novel strategy, lacustrine spawning was hypothesized for these eight Labeobarbus species. This hypothesis was further supported by observations of running female fishes in the littoral zones distant from any of the afferent rivers. This derived strategy is only common among the littoraldwelling Labeobarbus species with restricted distribution patterns. At present it is thought that sequential waves of speciation and habitat divergence followed by trophic specialization, shaped the diversity of Lake Tana labeobarbs.
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