Genetic diversity strategy for the management and use of rubber genetic resources: more than 1,000 wild and cultivated accessions in a 100-genotype core collection

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation

Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analyzed data from the Steller’s sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographical range and where both genetic samples and detailed demographic data have been collected from many diverse breeding colonies. To previously published mitochondrial DNA(mtDNA) and microsatellite data sets,we have added new data for amplified fragment length polymorphism (AFLP) markers, comprising 238 loci scored in 285 sea lions sampled from 23 natal rookeries. Genotypic diversity was low relative to most vertebrates, with only 37 loci (15.5%) being polymorphic. Moreover, contrasting geographical patterns of genetic diversity were found at the three markers, with Nei’s gene diversity tending to be higher for AFLPs and microsatellites in rookeries of the western and Asian stocks, while the highest mtDNA values were found in the eastern stock. Overall, and despite strongly contrasting demographic histories, after applying phylogenetic correction we found little correlation between genetic diversity and either colony size or demography. In contrast, we were able to show a highly significant positive relationship between AFLP diversity and current population size across a range of pinniped species, even though equivalent analyses did not reveal significant trends for either microsatellites or mtDNA.

Observations on Chromosomes of Dicrostonyx torquatus stevensoni Nelson and Chromosomal Diversity in Varying Lemmings = Untersuchungen an den Chromosomen von Dicrostonyx torquatus stevensoni Nelson und chromosomale Unterschiede bei Halsbandlemmingen

English abstract: The cytogenetic characteristics of the varying lemming, Dicrostonyx torquatus stevensoni, (2n = 34), were investigated, and diploid chromosomal numbers were reported for four other nominal subspecies (exsul, nelsoni, richardsoni, and rubricatus) of the torquatus-group in North America. The diploid complements ranged from 30 to 44 chromosomes, and the fundamental number from 50 to 55. Chromosomal polymorphism was observed in all forms. In cross-breeding experiments, the mating of F1 progeny was not productive. The findings support the zoogeographic concept that populations of Dicrostonyx became fragmented or displaced southward during Würm time, with relict stocks persisting in unglaciated refugia or periglacial tundra. Speciation in the isolates led to chromosomal evolution, with the result that populations spreading from refugia in post-glacial time are reproductively isolated. The torquatus-group in North America appears to be a superspecies. German title: Untersuchungen an den Chromosomen von Dicrostonyx torquatus stevensoni Nelson und chromosomale Unterschiede bei Halsbandlemmingen German abstract: Die cytogenetischen Merkmale des Halsbandlemmings, Dicrostonyx torquatus stevensoni, (2n = 34) wurden eingehend untersucht, und für vier andere nordamerikanische Unterarten der torquatus-Gruppe wurden die somatischen Chromosomensätze festgestellt. Die Chromosomenzahl der untersuchten Populationen schwankte zwischen 30 und 44, der NF (Nombre Fondamental) zwischen 50 und 55. Zuchttiere der verschiedenen Populationen wurden erfolgreich gekreuzt, aber Sterilität der F1 Unterartbastarde war typisch. Die Halsbandlemminge wiesen Karyotypenverschiedenheiten auf, die sich durch Variationen des Robertsonschen Typus, Deletionen oder möglicherweise durch perizentrische Inversionen erklären. Die Ergebnisse sprechen dafür, daß das ursprüngliche Verbreitungsgebiet von Dicrostonyx in Nordamerika durch die letzte (Würm) Vereisung getrennt wurde, und daß die Reliktpopulationen die letzte Glazial-Phase in eisfreien Refugien oder in periglazialer Tundra überlebten, wo Karyotypevolution durch lokale Anpassungsbedürfnisse gefördert wurde. Die in der Postglazialzeit aus den Refugien sich verbreitenden Populationen von Dicrostonyx scheinen reproduktiv isoliert zu sein. Die torquatus-Gruppe in Nordamerika gilt also als Superspecies.

THE EFFECT OF INTENSE LIGHT ON BIRD BEHAVIOR AND PHYSIOLOGY

It has been known for centuries that light (photoperiod) is possibly the major environmental stimuli affecting bird behavior and physiology. The length of the light period stimulates the breeding cycle, migration, fat deposition, and molt in most species of birds. Therefore, it is only natural that one would think of using light as a means of bird control. In fact, light has already been used as a bird control; flood-light traps have been used to trap blackbirds (Meanley 1971); Meanley states that 2000-W search lights have been used to alleviate depredation by ducks in rice fields. Pulsing light is already used on aircraft, aircraft hangers and high towers as a means of detourinq birds (Schaefer, 1968). With some positive results already obtained with light as a bird control, the next step is to see if a better light source (the laser) might not have a greater effect. The laser is basically an intense and coherent light with extreme directivity and, thus, might have greater influence on a bird’s behavioral and physiological responses.

Evaluating the legacy of landscape history: extinction debt and species credit in bird and small mammal assemblages in the Brazilian Atlantic Forest

There is now an extensive literature on extinction debt following deforestation. However, the potential for species credit in landscapes that have experienced a change from decreasing to expanding forest cover has received little attention. Both delayed responses should depend on current landscape forest cover and on species life-history traits, such as longevity, as short-lived species are likely to respond faster than long-lived species. We evaluated the effects of historical and present-day local forest cover on two vertebrate groups with different longevities understorey birds and non-flying small mammals - in forest patches at three Atlantic Forest landscapes. Our work investigated how the probability of extinction debt and species credit varies (i) amongst landscapes with different proportions of forest cover and distinct trajectories of forest cover change, and (ii) between taxa with different life spans. Our results suggest that the existence of extinction debt and species credit, as well as the potential for their future payment and/or receipt, is not only related to forest cover trajectory but also to the amount of remaining forest cover at the landscape scale. Moreover, differences in bird and small mammal life spans seem to be insufficient to affect differently their probability of showing time-delayed responses to landscape change. Synthesis and applications. Our work highlights the need for considering not only the trajectory of deforestation/regeneration but also the amount of forest cover at landscape scale when investigating time-delayed responses to landscape change. As many landscapes are experiencing a change from decreasing to expanding forest cover, understanding the association of extinction and immigration processes, as well as their interactions with the landscape dynamic, is a key factor to plan conservation and restoration actions in human-altered landscapes.

Environmental suitability of a highly fragmented and heterogeneous landscape for forest bird species in south-eastern Brazil

Assessment of the suitability of anthropogenic landscapes for wildlife species is crucial for setting priorities for biodiversity conservation. This study aimed to analyse the environmental suitability of a highly fragmented region of the Brazilian Atlantic Forest, one of the world's 25 recognized biodiversity hotspots, for forest bird species. Eight forest bird species were selected for the analyses, based on point counts (n = 122) conducted in April-September 2006 and January-March 2009. Six additional variables (landscape diversity, distance from forest and streams, aspect, elevation and slope) were modelled in Maxent for (1) actual and (2) simulated land cover, based on the forest expansion required by existing Brazilian forest legislation. Models were evaluated by bootstrap or jackknife methods and their performance was assessed by AUC, omission error, binomial probability or p value. All predictive models were statistically significant, with high AUC values and low omission errors. A small proportion of the actual landscape (24.41 +/- 6.31%) was suitable for forest bird species. The simulated landscapes lead to an increase of c. 30% in total suitable areas. In average, models predicted a small increase (23.69 +/- 6.95%) in the area of suitable native forest for bird species. Being close to forest increased the environmental suitability of landscapes for all bird species; landscape diversity was also a significant factor for some species. In conclusion, this study demonstrates that species distribution modelling (SDM) successfully predicted bird distribution across a heterogeneous landscape at fine spatial resolution, as all models were biologically relevant and statistically significant. The use of landscape variables as predictors contributed significantly to the results, particularly for species distributions over small extents and at fine scales. This is the first study to evaluate the environmental suitability of the remaining Brazilian Atlantic Forest for bird species in an agricultural landscape, and provides important additional data for regional environmental planning.

Morphological, molecular and cross-breeding analysis of geographic populations of coconut-mite associated predatory mites identified as Neoseiulus baraki: evidence for cryptic species?

Surveys were conducted in Brazil, Benin and Tanzania to collect predatory mites as candidates for control of the coconut mite Aceria guerreronis Keifer, a serious pest of coconut fruits. At all locations surveyed, one of the most dominant predators on infested coconut fruits was identified as Neoseiulus baraki Athias-Henriot, based on morphological similarity with regard to taxonomically relevant characters. However, scrutiny of our own and published descriptions suggests that consistent morphological differences may exist between the Benin population and those from the other geographic origins. In this study, we combined three methods to assess whether these populations belong to one species or a few distinct, yet closely related species. First, multivariate analysis of 32 morphological characters showed that the Benin population differed from the other three populations. Second, DNA sequence analysis based on the mitochondrial cytochrome oxidase subunit I (COI) showed the same difference between these populations. Third, cross-breeding between populations was unsuccessful in all combinations. These data provide evidence for the existence of cryptic species. Subsequent morphological research showed that the Benin population can be distinguished from the others by a new character (not included in the multivariate analysis), viz. the number of teeth on the fixed digit of the female chelicera.

Associations of Forest Cover, Fragment Area, and Connectivity with Neotropical Understory Bird Species Richness and Abundance

Theoretical and empirical studies demonstrate that the total amount of forest and the size and connectivity of fragments have nonlinear effects on species survival. We tested how habitat amount and configuration affect understory bird species richness and abundance. We used mist nets (almost 34,000 net hours) to sample birds in 53 Atlantic Forest fragments in southeastern Brazil. Fragments were distributed among 3 10,800-ha landscapes. The remaining forest in these landscapes was below (10% forest cover), similar to (30%), and above (50%) the theoretical fragmentation threshold (approximately 30%) below which the effects of fragmentation should be intensified. Species-richness estimates were significantly higher (F = 3715, p = 0.00) where 50% of the forest remained, which suggests a species occurrence threshold of 30-50% forest, which is higher than usually occurs (<30%). Relations between forest cover and species richness differed depending on species sensitivity to forest conversion and fragmentation. For less sensitive species, species richness decreased as forest cover increased, whereas for highly sensitive species the opposite occurred. For sensitive species, species richness and the amount of forest cover were positively related, particularly when forest cover was 30-50%. Fragment size and connectivity were related to species richness and abundance in all landscapes, not just below the 30% threshold. Where 10% of the forest remained, fragment size was more related to species richness and abundance than connectivity. However, the relation between connectivity and species richness and abundance was stronger where 30% of the landscape was forested. Where 50% of the landscape was forested, fragment size and connectivity were both related to species richness and abundance. Our results demonstrated a rapid loss of species at relatively high levels of forest cover (30-50%). Highly sensitive species were 3-4 times more common above the 30-50% threshold than below it; however, our results do not support a unique fragmentation threshold.

Genetic diversity and population structure of Musa accessions in ex situ conservation

Abstract Background Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. Results From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. Conclusions The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the “single-step domestication” hypothesis had long predominated. These findings will have an impact in future breeding approaches. Structure analysis enabled the efficient detection of ancestry of recently developed tetraploid hybrids by breeding programs, and for some triploids. However, for the main commercial subgroups, Structure appeared to be less efficient to detect the ancestry in diploid groups, possibly due to sampling restrictions. The possibility of inferring the membership among accessions to correct the effects of genetic structure opens possibilities for its use in marker-assisted selection by association mapping.

Functional markers for gene mapping and genetic diversity studies in sugarcane

Abstract Background The database of sugarcane expressed sequence tags (EST) offers a great opportunity for developing molecular markers that are directly associated with important agronomic traits. The development of new EST-SSR markers represents an important tool for genetic analysis. In sugarcane breeding programs, functional markers can be used to accelerate the process and select important agronomic traits, especially in the mapping of quantitative traits loci (QTL) and plant resistant pathogens or qualitative resistance loci (QRL). The aim of this work was to develop new simple sequence repeat (SSR) markers in sugarcane using the sugarcane expressed sequence tag (SUCEST database). Findings A total of 365 EST-SSR molecular markers with trinucleotide motifs were developed and evaluated in a collection of 18 genotypes of sugarcane (15 varieties and 3 species). In total, 287 of the EST-SSRs markers amplified fragments of the expected size and were polymorphic in the analyzed sugarcane varieties. The number of alleles ranged from 2-18, with an average of 6 alleles per locus, while polymorphism information content values ranged from 0.21-0.92, with an average of 0.69. The discrimination power was high for the majority of the EST-SSRs, with an average value of 0.80. Among the markers characterized in this study some have particular interest, those that are related to bacterial defense responses, generation of precursor metabolites and energy and those involved in carbohydrate metabolic process. Conclusions These EST-SSR markers presented in this work can be efficiently used for genetic mapping studies of segregating sugarcane populations. The high Polymorphism Information Content (PIC) and Discriminant Power (DP) presented facilitate the QTL identification and marker-assisted selection due the association with functional regions of the genome became an important tool for the sugarcane breeding program.

Influence of habitat and climate change on European bird communities

Die Fragmentierung von Waldgebieten, der Verlust geeigneter Habitate, die Invasion exotischer Arten und globale Klimaveränderung haben auf Artengemeinschaften erhebliche Auswirkungen. Vögel dienen in vielen Fällen als Indikatorarten für Umweltveränderungen und, besonders, für Veränderungen im Zusammenhang mit globaler Erwärmung. In meiner Arbeit habe ich zuerst einen Literaturüberblick über die Auswirkungen globaler Klimaveränderung auf die Verbreitungsgebiete, den Artenreichtum und die Zusammensetzung von Vogelgemeinschaften dargestellt. Zahlreiche Untersuchungen zeigen, daß die Grenzen der Verbreitungsgebiete der meisten Vogelarten mit klimatischen Faktoren korrelieren. Verschiebungen der Verbreitungsgebiete in nördliche Richtung oder in höhere Regionen im Gebirge konnten bereits für viele temperate Vogelarten beobachtet werden. Weiterhin wurde ein zunehmender Artenreichtum besonders in nördlichen Breiten und in höheren Lagen für viele temperate Vogelgemeinschaften vorhergesagt. In trockenen Gebieten ist dagegen mit einer Abnahme des Artenreichtums zu rechnen. Im zweiten Teil meiner Arbeit habe ich untersucht, ob beobachtete Veränderungen in der Zusammensetzung europäischer Vogelgemeinschaften tatsächlich durch aktuelle Klimaveränderungen beeinflußt werden. Das Zugverhalten der Arten war dabei ein Schwerpunkt der Untersuchung, weil zu erwarten war, daß Vogelarten mit verschiedenem Zugverhalten unterschiedlich auf Klimaveränderungen reagieren. Ich habe ein Regressionsmodell genutzt, welches die räumliche Beziehung zwischen dem Anteil von Langstreckenziehern, Kurzstreckenziehern und Standvögeln in europäischen Vogelgemeinschaften und verschiedenen Klimavariablen beschreibt. Für 21 Gebiete in Europa habe ich Daten über beobachtete Veränderungen in der Struktur der Vogelgemeinschaften und isochrone Klimaveränderungen zusammengetragen. Mit Hilfe dieser Klimaveränderungen und dem räumlichen Regressionsmodell konnte ich berechnen, welche Veränderungen in den Vogelgemeinschaften aufgrund der veränderten Klimabedingungen zu erwarten wären und sie mit beobachteten Veränderungen vergleichen. Beobachtete und berechnete Veränderungen korrelierten signifikant miteinander. Die beobachteten Veränderungen konnten nicht durch räumliche Autokorrelationseffekte oder durch alternative Faktoren, wie z.B. Veränderungen in der Landnutzung, erklärt werden. Im dritten Teil der Arbeit untersuchte ich für eine mitteleuropäische Vogelgemeinschaft welchen Einfluß Habitatveränderungen, die Invasion exotischer Arten und die Klimaveränderung auf Veränderungen der Häufigkeit und Verbreitungsgröße der 159 Vogelarten am Bodensee zwischen 1980-1981 und 2000-2002 hatten. Dabei konnte gezeigt werden, daß Veränderungen in der regionalen Abundanz sowohl durch Habitatveränderungen als auch durch Klimavänderungen hervorgerufen wurden. Exotische Arten schienen in dieser Zeit keinen bedeutenden Einfluß zu haben. Besonders bei Agrarlandarten, Arten mit nördlicheren Verbreitungsgebieten und bei Langstreckenziehern konnten signifikante Abnahmen in der Abundanz beobachtet werden. Vor allem die anhaltenden negativen Bestandsveränderungen bei Langstreckenziehern und die in den letzten zehn Jahren aufgetretenen Abnahmen nördlicher verbreiteter Vogelarten deuten darauf hin, daß die Klimaveränderung aktuell als der größte Einfluß für Vögel in Europa angesehen werden muß. Insgesamt zeigen die Ergebnisse dieser Arbeit, daß sich der anhaltende Druck auf die Umwelt in erster Linie durch Habitat- und Klimaveränderungen manifestiert.

Macroecology of avian frugivore diversity

Die Verbreitung von Vögeln kann von sehr unterschiedlichen Faktoren (z.B. Habitatstruktur, Klima, Nahrungsverfügbarkeit, Evolutionsgeschichte) beeinflusst werden, die zudem auf verschiedenen räumlichen Skalen (lokal bis global) unterschiedlich wirken. In dieser Dissertation wurde die Artenvielfalt früchtefressender Vogelarten auf regionalem, kontinentalem und globalem Maßstab untersucht und getestet ob sie von Habitatstruktur (Landnutzung, Topographie, Vegetationsstruktur), Klima (Temperatur, Niederschlag, Evapotranspiration), Nahrungsressourcen (früchtetragende Baumarten), oder historischen Faktoren (biogeographische Region) bestimmt wird. Dazu wurden umfangreiche geographische Datenbanken auf verschiedenen räumlichen Skalen, d.h. auf regionalem (Kenia), kontinentalem (Afrika), und globalem (Welt) Maßstab, ausgewertet, die die Verbreitung aller Vogelarten und wichtiger Umweltfaktoren enthalten. Statistische Analysen auf globalem Maßstab zeigten, dass die Verbreitung von Früchtefressern sehr gut mit klimatischen Variablen, insbesondere aktueller Evapotranspiration und Produktivität, beschrieben werden kann. Unterschiede zwischen biogeographischen Regionen bleiben jedoch bestehen auch wenn für klimatische Unterschiede zwischen den Regionen korrigiert wird. Weiter zeigen unterschiedliche Ordnungen mit früchtefressenden Vogelarten unterschiedliche Diversifizierungsmuster. Dies deutet darauf hin, dass auch historische Faktoren, wie die Klima- und Evolutionsgeschichte, eine wichtige Rolle spielen. Analysen auf regionalem und kontinentalem Maßstab legen nahe, dass klimatische Faktoren im Wesentlichen indirekt auf die Artenvielfalt von Früchtefressern wirken, und zwar durch funktionelle Beziehungen zwischen Früchtefressern und Bäumen (z.B. trophische Interaktionen mit wichtigen Nahrungspflanzen, Vegetationsstruktur). Die Ergebnisse dieser Dissertation zeigen, dass biotische Interaktionen, direkte und indirekte klimatische Effekte, und das Zusammenwirken von Evolutionsgeschichte und heutigen Umweltbedingungen untersucht werden müssen um den Artenreichtum von Vögeln auf großem räumlichem Maßstab zu verstehen.

Molecular strategies for genetic diversity analysis and development of markers linked to resistance traits in apple

The goal of many plant scientists’ research is to explain natural phenotypic variation in term of simple changes in DNA sequence. DNA-based molecular markers are extensively used for the construction of genome-wide molecular maps and to perform genetic analysis for simple and complex traits. The PhD thesis was divided into two main research lines according to the different approaches adopted. The first research line is to analyze the genetic diversity in an Italian apple germplasm collection for the identification of markers tightly linked to targeted genes by an association genetic method. This made it possible to identify synomym and homonym accessions and triploids. The fruit red skin color trait has been used to test the reliability of the genetic approaches in this species. The second line is related to the development of molecular markers closely linked to the Rvi13 and Rvi5 scab resistance genes, previously mapped on apple’s chromosome 10 and 17 respectively by using the traditional linkage mapping method. Both region have been fine-mapped with various type of markers that could be used for marker-assisted selection in future breeding programs and to isolate the two resistance genes.