Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics

Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns of three ecologically divergent eucalypts sampled across a habitat fragmentation gradient in southern Australia. We demonstrate increased selfing and decreased pollen diversity with increased fragmentation for two small-insect-pollinated eucalypts, but no such relationship for the mobile-bird-pollinated eucalypt. In a meta-analysis, we then show that fragmentation generally does increase selfing rates and decrease pollen diversity, and that more mobile pollinators tended to dampen these mating-pattern shifts. Together, our findings support the premise that variation in pollinator form contributes to the diversity of mating-pattern responses to habitat fragmentation.     

Fragmentation genetics in tropical ecosystems: from fragmentation genetics to fragmentation genomics

Tropical regions are experiencing unprecedented economic and population growth. This goes hand in hand with increase habitat fragmentation of tropical ecosystems. Understanding the genetic consequences of these spatial and temporal changes across landscapes is critical to conservation of the vast majority of global biodiversity. This virtual issue of Conservation Genetics, presents six empirical and one review paper showcasing fascinating and important findings with regard to how habitat fragmentation impacts on genetic diversity in rare or endangered tropical species. The message from these papers is clear, fragmentation has a number of serious genetic consequences, which can contribute to undermining the viability of species in fragmented landscapes. Conservation genetics provides a powerful tool to inform both conservation and management of species and genetic resources. But, careful consideration is needed to ensure studies apply appropriate sampling designs and genetic analysis to better test hypothesis. Next generation genomics offers great opportunities to provide even more answers and greater resolution of the consequences for adaptive genetic variation, to ensure future tropical landscapes are resilient.     

Streptomyces genetics: a genomic perspective

Streptomycetes are gram-positive, soil-inhabiting bacteria of the order Actinomycetales. These organisms exhibit an unusual, developmentally complex life cycle and produce many economically important secondary metabolites, such as antibiotics, immunosuppressants, insecticides, and anti-tumor agents. Streptomyces species have been the subject of genetic investigation for over 50 years, with many studies focusing on the developmental cycle and the production of secondary metabolites. This information provides a solid foundation for the application of structural and functional genomics to the actinomycetes. The complete DNA sequence of the model organism, Streptomyces coelicolor M145, has been published recently, with others expected to follow soon. As more genomic sequences become available, the rational genetic manipulation of these organisms to elucidate metabolic and regulatory networks, to increase the production of commercially important compounds, and to create novel secondary metabolites will be greatly facilitated. This review presents the current state of the field of genomics as it is being applied to the actinomycetes.     

森林破碎化对鼠类—种子互作网络的影响

森林碎片化严重威胁生态系统的健康,导致物种多样性、生态系统稳定性的降低。鼠类和森林种子是一类重要的互作网络,在生物多样性维持和生态系统服务功能上发挥着重要作用,有关森林斑块大小及演替阶段对鼠类—种子互作网络的影响的报道较少。本研究以都江堰地区亚热带森林鼠类—种子互作系统为例,选取15个不同大小和演替阶段的森林斑块,结合红外相机监测和种子标记,通过监测鼠类与种子的互作过程,分析了斑块大小和演替阶段对鼠类—种子互作关系的影响,并绘制了各斑块鼠类—种子互作网络图谱,发现:中斑块(2-4 hm~2)森林中鼠类的物种数最多,大斑块(9-30 hm~2)最少;演替后期(20-40 yrs)次生林的加权嵌套度(Weighted-Interaction Nestedness Estimator,WINE)显著地高于演替早期(10-20 yrs)次生林;原始林网络内相关植物的植株总数和胸径(DBH)总和都要显著大于次生林。我们的结果说明森林破碎化对鼠类—种子互作网络的加权嵌套度有一定影响,对其他网络参数影响不大,可能与其种间关系泛化度较大有关。该结果对进一步研究种间互作关系及生态网络结构与功能具有一定的参考意义。     

Epigenome dynamics: a quantitative genetics perspective

Classically, quantitative geneticists have envisioned DNA sequence variants as the only source of heritable phenotypes. This view should be revised in light of accumulating evidence for widespread epigenetic variation in natural and experimental populations. Here we argue that it is timely to consider novel experimental strategies and analysis models to capture the potentially dynamic interplay between chromatin and DNA sequence factors in complex traits.     

The genetics of lupus: a functional perspective

Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component and is characterized by chronic inflammation and the production of anti-nuclear auto-antibodies. In the era of genome-wide association studies (GWASs), elucidating the genetic factors present in SLE has been a very successful endeavor; 28 confirmed disease susceptibility loci have been mapped. In this review, we summarize the current understanding of the genetics of lupus and focus on the strongest associated risk loci found to date (P <1.0 × 10−8). Although these loci account for less than 10% of the genetic heritability and therefore do not account for the bulk of the disease heritability, they do implicate important pathways, which contribute to SLE pathogenesis. Consequently, the main focus of the review is to outline the genetic variants in the known associated loci and then to explore the potential functional consequences of the associated variants. We also highlight the genetic overlap of these loci with other autoimmune diseases, which indicates common pathogenic mechanisms. The importance of developing functional assays will be discussed and each of them will be instrumental in furthering our understanding of these associated variants and loci. Finally, we indicate that performing a larger SLE GWAS and applying a more targeted set of methods, such as the ImmunoChip and next generation sequencing methodology, are important for identifying additional loci and enhancing our understanding of the pathogenesis of SLE.     

The impact of forest area fragmentation on ant population

The paper presents an analysis of the impact of some morphological and ecological factors on the spatial distribution of 19 ant species populating fragmented forest areas within an urban territory. Twofold reduction of the species composition in small forested fragments with an area less than 5000 m² was shown. The highest density of ant anthills against the background of a high degree of species diversity similar to that in the slightly fragmented territories was found in median fragments with an area varying from 10000 to 250000 m². The influence of anthill construction diversity and size of workers on the resistance of species to area reduction was revealed. Species with 3–5 mm long workers that dwell in nests with and without epiterranean hills were more tolerant to the fragmentation than species with big workers (> 8 mm long) dwelling only in anthills with epiterranean hills composed of vegetable and mineral particles.     

Forest fragmentation truncates a food chain based on an old-growth forest bracket fungus

We studied the effect of forest fragmentation on the insect community inhabiting an old-growth forest specialist bracket fungus, Fomitopsis rosea , in eastern Finland. Samples of the fungus from large non-isolated control areas were compared with samples from forest fragments in two isolation time classes; 2–7 yr and 12–32 yr since isolation. Fomitopsis rosea hosted a species-rich community with relatively many specialized old-growth forest insects. The numerically dominant food chain consisted of F. rosea , the tineid moth Agnathosia mendicella and the tachinid fly Elfia cingulata , a specialist parasitoid of A. mendicella . The frequency of F. rosea on suitable fallen spruce logs and the frequency of A. mendicella in fruiting bodies were significantly lower in the forest fragments than in the control areas. The median number of trophic levels decreased from three in the control areas to one in the fragments that had been isolated for the longest period of time. The parasitoid was completely missing from the fragments isolated for 12–32 yr. Our results show that in boreal forests habitat loss and fragmentation truncate food chains of specialized species in the course of time since isolation.     

Population genetics of Formica aquilonia wood ants in Scotland: the effects of long-term forest fragmentation and recent reforestation

Formica aquilonia wood ants are forest specialists which play a key role in the ecology of forests in Europe. Many of the Scottish populations at the edge of the species distribution range occur in highly fragmented landscapes. We used ten microsatellite loci to study the genetic diversity and structure of populations from two contrasting regions (Inverpolly and the Trossachs) to set the Scottish populations in the context of conspecific populations in mainland Europe. Historically, both study regions have experienced extreme habitat loss and fragmentation over several centuries. Inverpolly has remained fragmented whereas large scale reforestation over the last century has greatly increased the forested area in the Trossachs. Despite the long history of fragmentation, genetic diversity in the Scottish populations was greater than in the populations in mainland Europe. Genetic diversity was similar in the two Scottish regions and no evidence of inbreeding was detected. However, the populations in Inverpolly showed more evidence of genetic bottlenecks, possibly due to more frequent stochastic events such as moorland fires. The ant populations in individual forests were genetically distinct and we detected no contemporary gene flow between forests. The most intensively studied forest where non-native conifer plantations now occupy the matrix between the remaining ancient woodland fragments showed evidence that admixture and gene flow between nests was reducing the past differentiation. This may reflect a dynamic response to the reconnection of previously isolated populations in forest fragments by recent reforestation.     

Landscape genetics of the self-compatible forest herb Geum urbanum: effects of habitat age, fragmentation and local environment

To investigate the role of habitat fragmentation, fragment age and local environment in shaping the genetics of plant populations, we examined the genetic structure of the self-compatible forest herb Geum urbanum using microsatellite markers. A historical land-use reconstruction assigned the studied populations to two age classes: populations in primary forest fragments, and populations in secondary fragments. Local environmental conditions were quantified on the basis of the herb-layer community composition. A stepwise general linear model revealed that levels of within-population genetic diversity were best explained by population size, landscape connectivity and the interaction between both. Connectivity was positively correlated with the genetic diversity of small populations, but did not significantly affect the diversity of large populations. Contrary to what we expected, secondary-forest populations showed lower divergence relative to populations located in primary patches. Small populations were genetically more diverged compared to large populations. Mantel tests showed no significant isolation by distance and no significant correlation between habitat similarity and genetic differentiation. We conclude that gene flow has probably prevented founder events from being reflected in the present genetic structure of G. urbanum. Gene flow towards low-connectivity populations, however, seemed to be insufficient to counteract the effects of drift in small populations.     

Approaches to prokaryotic biodiversity: a population genetics perspective

The study of prokaryotic diversity has blossomed during the last 10-15 years as a result of the introduction of molecular identification, mostly based on direct 16S rRNA gene polymerase chain reaction (PCR) amplification and sequencing from natural samples. A large amount of information exists about the diversity of this specific gene. However, data from the field of bacterial population genetics and genomics make questionable the value of information regarding just one gene. Even if we accept 16S rRNA genes as useful for species identification, intraspecific variation in bacteria is so high that species catalogues are often of little value. The gene pools represented by an operational species are yet impossible to predict. On the other hand, adaptive features in prokaryotes are often coded in gene clusters (genomic islands) that can be cloned directly from the environment, sequenced and even expressed in a surrogate host. Thus, the study of the environmental genome or metagenome appears as an alternative that could eventually lead to a more realistic understanding of prokaryotic biodiversity, provide biotechnology with new tools and maybe even contribute to develop a model of prokaryotic evolution.     

The genetics of bladder cancer: a cytogeneticist's perspective

Cytogenetic studies of bladder cancer have helped to define two clinically distinct subtypes: benign tumors with few genetic mutations and a stable karyotype and aggressive cancers with chromosomal instability and many non-random cytogenetic aberrations. While the cytogenetic data does not provide complete information, these studies have been important for suggesting pathways for bladder carcinoma initiation and its progression. In addition, molecular cytogenetic studies have proven useful for diagnosing bladder cancer and for monitoring patients for cancer recurrence. More detailed molecular genetic studies and expression array analyses are needed to fully comprehend the biologic processes associated with urothelial cancers, but cytogenetics studies have laid the foundation for further investigation.     

Effects of forest fragmentation on genetic variation in endemic understory forest birds in central Madagascar

Summary This study focuses on some genetic consequences of habitat fragmentation in populations of four endemic bird species (Monticola sharpei, Terpsiphone mutata, Foudia omissa, andFoudia madagascariensis) living in the understory of forests in the Réserve Spéciale d'Ambohitantely on the Central High Plateau of Madagascar. The four species differ in their dependency on forest habitats, which may be related to their migration abilities between isolated forest fragments. Genetic variation was analysed on the basis of multi-locus fingerprints in order to study the influence of migration and habitat size on the genetic variability of local populations. There was no evidence that forest fragmentation affects any of the four species with respect to genetic variability.

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Effekte von Waldfragmentation auf die genetische Variabilität endemischer Vogelarten in Zentral-Madagaskar

Zusammenfassung Rund 53 % der Vogelarten Madagaskars sind endemisch. Viele dieser Arten sind an Waldhabitate gebunden und durch die Verinselung der madagassischen Wälder hochgradig bedroht. In dem vorliegenden Projekt wird die Auswirkung der Verinselung auf die genetische Variabilität und die genetische Differenzierung von vier endemischen Vogelarten am Beispiel des Reservats von Ambohitantely im zentralen Hochland Madagaskars untersucht. Ambohitantely beinhaltet mehr als 500 Waldfragmente von 0,64 ha bis 1250 ha. Untersucht wurden: 1. die WaldartFoudia omissa, 2.Monticola (früherPseudocossyphus)sharpei, eine Art mit starker Bevorzugung für primäre Waldlebensräume, die aber gelegentlich auch in Sekundärvegetation auftritt, sowie 3.Terpsiphone mutata und 4.Foudia madagascariensis, beides Arten, die sowohl in Wäldern als auch in offenen Landschaften vorkommen. Die unterschiedliche Abhängigkeit dieser Arten von Waldhabitaten und der damit verbundenen Möglichkeit, offene Landschaften zwischen den Waldfragmenten zu überbrücken, führte zur Frage, ob die Verinselung die genetische Vielfalt der untersuchten Populationen beeinflußt. Für die genetischen Analysen wurden Blutproben von Tieren aus drei Gebieten mit 1250 ha, 136 ha und 28 ha gesammelt. Die Proben wurden mit Multilocus-Fingerprints genetisch charakterisiert. Zum Untersuchungszeitpunkt konnte kein Einfluß der Fragmentierung auf die genetische Populationsstruktur der vier untersuchten Arten nachgewiesen werden.