Rock outcrop orchids reveal the genetic connectivity and diversity of inselbergs of northeastern Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic resource impacts of habitat loss and degradation; reconciling empirical evidence and predicted theory for neotropical trees

The theoretical impacts of anthropogenic habitat degradation on genetic resources have been well articulated. Here we use a simulation approach to assess the magnitude of expected genetic change, and review 31 studies of 23 neotropical tree species to assess whether empirical case studies conform to theory. Major differences in the sensitivity of measures to detect the genetic health of degraded populations were obvious. Most studies employing genetic diversity (nine out of 13) found no significant consequences, yet most that assessed progeny inbreeding (six out of eight), reproductive output (seven out of 10) and fitness (all six) highlighted significant impacts. These observations are in line with theory, where inbreeding is observed immediately following impact, but genetic diversity is lost slowly over subsequent generations, which for trees may take decades. Studies also highlight the ecological, not just genetic, consequences of habitat degradation that can cause reduced seed set and progeny fitness. Unexpectedly, two studies examining pollen flow using paternity analysis highlight an extensive network of gene flow at smaller spatial scales (less than 10 km). Gene flow can thus mitigate against loss of genetic diversity and assist in long-term population viability, even in degraded landscapes. Unfortunately, the surveyed studies were too few and heterogeneous to examine concepts of population size thresholds and genetic resilience in relation to life history. Future suggested research priorities include undertaking integrated studies on a range of species in the same landscapes; better documentation of the extent and duration of impact; and most importantly, combining neutral marker, pollination dynamics, ecological consequences, and progeny fitness assessment within single studies.

Evolutionary experiments on mate recognition in the Drosophila serrata species complex

It is becoming increasingly apparent that at least some aspects of the evolution of mate recognition may be amenable to manipulation in evolutionary experiments. Quantitative genetic analyses that focus on the genetic consequences of evolutionary processes that result in mate recognition evolution may eventually provide an understanding of the genetic basis of the process of speciation. We review a series of experiments that have attempted to determine the genetic basis of the response to natural and sexual selection on mate recognition in the Drosophila serrata species complex. The genetic basis of mate recognition has been investigated at three levels: (1) between the species of D. serrata and D. birchii using interspecific hybrids, (2) between populations of D. serrata that are sympatric and allopatric with respect to D. birchii, and (3) within populations of D. serrata. These experiments suggest that it may be possible to use evolutionary experiments to observe important events such as the reinforcement of mate recognition, or the generation of the genetic associations that are central to many sexual selection models.

Spatial structure and habitat variation in a grasshopper hybrid zone

A hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae) in northern Spain has been analyzed for variation in morphology and ecology. These species are readily distinguished by the number of stridulatory pegs on the hind femur. Both sexes are fully winged and inhabit disturbed habitats throughout the study area. We develop a maximum-likelihood approach to fitting a two-dimensional cline to geographical variation in quantitative traits and for estimating associations of population mean with local habitat. This method reveals a cline in peg number approximately 30 km south of the Picos de Europa Mountains that shows substantial deviations in population mean compared with the expectations of simple tension zone models. The inclusion of variation in local vegetation in the model explains a significant proportion of the residual variation in peg number, indicating that habitat-genotype associations contribute to the observed spatial pattern. However, this association is weak, and a number of populations continue to show strong deviations in mean even after habitat is included in the final model. These outliers may be the result of long-distance colonization of sites distant from the cline center or may be due to a patchy pattern of initial contact during postglacial expansion. As well as contrasting with the smooth hybrid zones described for Chorthippus parallelus, this situation also contrasts with the mosaic hybrid zones observed in Gryllus crickets and in parts of the hybrid zone between Bombina toad species, where habitat-genotype associations account for substantial amounts of among-site variation.

Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish, Polynemus sheridani

We assayed mtDNA haplotype [300 base pairs (bp) control region] geography and genealogy in the Indo-Pacific tasselfish, Polynemus sheridani from its contiguous estuarine distribution across northern Australia (n = 169). Eight estuaries were sampled from three oceanographic regions (Timor Sea, Gulf of Carpentaria and the Coral Sea) to assess the impact of Pleistocene sea level changes on the historical connectivity among P. sheridani populations. Specifically, we investigated the genetic consequences of disruption to Indian-Pacific Ocean connectivity brought about by the closure of the Torres Strait. Overall there was significant population subdivision among estuaries (F-ST = 0.161, (Phi(ST) = 0.187). Despite a linear distribution, P. sheridani did not show isolation by distance over the entire sampled range because of genetic similarity of estuaries greater than 3000 km apart. However, significant isolation by distance was detected between estuaries separated by less than 3000 km of coastline. Unlike many genetic studies of Indo-Pacific marine species, there was no evidence for an historical division between eastern and western populations. Instead, phylogeographical patterns were dominated by a starlike intraspecific phylogeny coupled with evidence for population expansion in both the Gulf of Carpentaria and the Coral Sea but not the Timor Sea. This was interpreted as evidence for recent west to east recolonization across of northern Australia following the last postglacial marine advance. We argue that although sufficient time has elapsed postcolonization for populations to approach gene flow-drift equilibrium over smaller spatial scales (< 3000 km), the signal of historical colonization persists to obscure the expected equilibrium pattern of isolation by distance over large spatial scales (> 3000 km).

Impact of social structure variation on population genetics, social conflicts and life histories in ants

Summary The evolution of social structures and breeding systems in animals is a complex process that combines ecological, genetical and social factors. This thesis sheds light on important changes in population genetics, life-history and social behavior that are associated with variation in social structure in ants. The socially polymorphic ant Formica selysi was chosen as the model organism because single- and multiple-queen colonies occur in close proximity within a single large population. The shift from single- to multiple-queen colonies is generally associated with profound changes in dispersal behavior and mode of colony founding. In chapter 1, we examine the genetic consequences of variation in social structure at both the colony and population levels. A detailed microsatellite analysis reveals that both colony types have similar mating systems, with few or no queen turnover. Furthermore, the complete lack of genetic differentiation observed between single- and multiple-queen colonies provides no support to the hypothesis that change in queen number leads to restricted gene flow between social forms. Besides changes in the genetic composition of the colony, the variation in the number of queens per colony is associated with changes in a network of behavioral and life-history traits that have been described as forming a "polygyny syndrome". In chapter 2, we demonstrate that multiple-queen colonies profoundly differ from single-queen ones in terms of size, nest density and lifespan of colonies, in weight of queens produced, as well as in allocation to reproductive individuals relative to workers. These multifaceted changes in life-history traits can provide various fitness benefits to members of multiple-queen colonies. Increasing the number of queens in a colony usually results in a decreased level of aggression towards non-nestmates. The phenotype matching hypothesis predicts that, compared to single-queen colonies, multiple-queen colonies have more diverse genetically-derived cues used for recognition, resulting in a lower ability to discriminate non-nestmates. In sharp contrast to this hypothesis, we show in chapter 3 that single- and multiple-queen colonies exhibit on average similar levels of aggression. Moreover, stronger aggression is recorded between colonies of different social structure than between colonies of the same social structure. Several hypotheses propose that the evolution of multiple-queen colonies is at least partly due to benefits resulting from an increase in colony genetic diversity. The task-efficiency hypothesis holds that genetic variation improves task performance due to a more complete or more sensitive expression of the genetically-based division of labor. In .chapter 4, we evaluate if higher colony genetic diversity increases worker size polymorphism and thus may improve division of labor. We show that despite the fact that worker size has a heritable component, higher levels of genetic diversity do not result in more polymorphic workers. The smaller size and lower polymorphism levels of workers of multiple-queen colonies compared to single-queen ones further indicate that an increase in colony genetic diversity does not increase worker size polymorphism but might improve colony homeostasis. In chapter 5, we provide clear evidence for an ongoing conflict between queens and workers on sex allocation, as predicted by kin selection theory. Our data show that queens of F. selysi strongly influence colony sex allocation by biasing the sex ratio of their eggs. However, there is also evidence that workers eliminated some male brood, resulting in a population sex-investment ratio that is between the queens' and workers' equilibria. Résumé L'évolution des structures sociales et systèmes d'accouplement chez les animaux est un processus complexe combinant à la fois des facteurs écologiques, génétiques et sociaux. Cette thèse met en lumière des changements importants dans la génétique des populations, les traits d'histoire de vie et les comportements sociaux qui sont associés à des variations de structure sociale chez les fourmis. Durant ce travail, nous avons étudié une population de Formica selysi composée à la fois de colonies à une reine et de colonies à plusieurs reines. La transition de colonie à une reine à colonie à plusieurs reines est généralement associée à des changements profonds dans le comportement de dispersion ainsi que le mode de fondation des sociétés. Dans le chapitre 1, nous examinons les conséquences génétiques de la variation de structure sociale tant au niveau de la colonie qu'au niveau de la population. Une analyse détaillée à l'aide de marqueurs microsatellites nous révèle que les deux types de colonies ont des systèmes d'accouplements similaires avec peu ou pas de renouvellement de reines. L'absence totale de différenciation génétique entre les colonies à une et à plusieurs reines n'apporte aucun support à l'hypothèse selon laquelle un changement dans le nombre de reines conduit à un flux de gènes restreint entre les deux formes sociales. A côté de changements dans la composition génétique de la colonie, la variation du nombre de reines dans une colonie est associée à une multitude de changements comportementaux et de traits d'histoire de vie qui ont été décrits comme formant un "syndrome polygyne". Dans le chapitre 2, nous démontrons que les colonies à plusieurs reines diffèrent profondément des colonies à une reine en terme de taille, densité de nids, longévité des colonies, poids des nouvelles reines produites ainsi que dans l'allocation entre les individus reproducteurs et les ouvrières. Ces changements multiples dans les traits d'histoire de vie peuvent apporter des bénéfices variés en terme de fitness aux colonies à plusieurs reines. L'augmentation du nombre de reines dans une colonie est généralement associée à une baisse du degré d'agressivité envers les fourmis étrangères au nid. L'hypothèse "phénotype matching" prédit que les colonies à plusieurs reines ont une plus grande diversité dans les facteurs d'origine génétique utilisés pour la reconnaissance, résultant en une capacité diminuée à discriminer une fourmi étrangère au nid. Contrairement à cette hypothèse, nous montrons dans le chapitre 3 que les colonies à une et à plusieurs reines ont des niveaux d'agressivité similaires. De plus, une agressivité accrue est observée entre colonies de structures sociales différentes comparée à des colonies de même structure sociale. Plusieurs hypothèses ont proposé que l'évolution de colonies ä plusieurs reines soit en partie due aux bénéfices résultant d'une augmentation de la diversité génétique dans la colonie. L'hypothèse "task efficiency" prédit que la diversité génétique améliore l'efficacité à effectuer certaines tâches grâce à une expression plus complète et plus souple d'une division du travail génétiquement déterminée. Nous évaluons dans le chapitre 4 si un accroissement de la diversité génétique augmente le polymorphisme de taille des ouvrières, d'où peut ainsi découler une meilleure division du travail. Nous montrons qu'en dépit du fait que la taille des ouvrières soit un caractère héritable, une forte diversité génétique ne se traduit pas par un plus fort polymorphisme chez les ouvrières. Les ouvrières de colonies à plusieurs reines sont plus petites et moins polymorphes que celles des colonies à une seule reine. Dans le chapitre 5, nous démontrons l'existence d'un conflit ouvert entre reines et ouvrières à propos de l'allocation dans les sexes, comme le prédit la théorie de la sélection de parentèle. Nos données révèlent que les reines de F. selysi influencent fortement l'allocation dans les sexes en biaisant la sexe ratio des oeufs. Cependant, certains indices indiquent que les ouvrières éliminent une partie du couvain mâle, ce qui a pour effet d'avoir un investissement dans les sexes au niveau de la population intermédiaire entre les intérêts des reines et des ouvrières.

Manipulating sex ratio to increase population growth: the example of the Lesser Kestrel

Small or decreasing populations call for emergency actions like, for example, captive breeding programs. Such programs aim at rapidly increasing population sizes in order to reduce the loss of genetic variability and to avoid possible Allee effects. The Lesser Kestrel Falco naumanni is one of the species that is currently supported in several captive breeding programs at various locations. Here, we model the demographic and genetic consequences of potential management strategies that are based on offspring sex ratio manipulation. Increased population growth could be achieved by manipulating female conditions and/or male attractiveness in the captive breeders and consequently shifting the offspring sex ratio towards more female offspring, which are then used for reintroduction. Fragmenting populations into wild-breeding and captive-breeding demes and manipulating population sex ratio both immediately increase the inbreeding coefficient in the next generation (i.e. decrease N-e) but may, in the long term, reduce the loss of genetic variability if population growth is restricted by the number of females. We use the Lesser Kestrel and the wealth of information that is available on this species to predict the long-term consequences of various kinds of sex-ratio manipulation. We find that, in our example and possibly in many other cases, a sex-ratio manipulation that seems realistic could have a beneficial effect on the captive breeding program. However, the possible long-term costs and benefits of such measures need to be carefully optimized.

Demogenetics in metapopulations

SUMMARY : Human-induced habitat fragmentation constitutes a major threat to biodiversity. Small and isolated populations suffer from increased stochasticity and from limited rescue effects. These two factors may be sufficient to cause local extinctions but fragmentation induces some genetic consequences that can also contribute significantly to extinction risks. Increased genetic drift reduces the effectiveness of selection against deleterious mutations, leading to their progressive accumulation. Drift also decreases both the standing genetic variation and the rate of fixation of beneficial mutations, limiting the evolutionary potential of isolated populations. Demography and genetics further interact and feed back on each other, progressively driving fragmented populations into "extinction vortices". The aim of the thesis was to better understand the processes occurring in fragmented populations. For this, I combined simulation studies and empirical data from three species that live in structured habitats. Chapter 1 and 2 investigate the demography of two shrew species in fragmented habitats. I showed that connectivity and habitat quality strongly affect the demography of the greater white-tooted shrew, although demographic stochasticity was extremely high. I also demonstrated that habitat fragmentation is one of the leading factors allowing the local coexistence of two competing shrew species. Chapter 3 and 4 focus on measuring connectivity in fragmented populations based on genetic data. In particular, I showed that genetic data can be used to detect the landscape elements impeding dispersal. In Chapter 5 that deals with the accumulation of deleterious mutations in fragmented populations, I demonstrated that mutation accumulation, as well a time to extinction, can be predicted from simple demographic and genetic measures. In the last two chapters, I monitored individual reproductive success in an isolated tree frogs population. These data allowed quantifying the effective population size, a measure closely linked to population evolutionary potential. To conclude, this thesis brings some new insights into the processes occurring in fragmented populations, and I hope it will contribute to the improvement of the management and conservation of fragmented populations.

Climatic oscillations shape the phylogeographical structure of Atlantic Forest fire-eye antbirds (Aves: Thamnophilidae)

In the present study, mitochondrial (mt)DNA sequence data were used to examine the genetic structure of fire-eye antbirds (genus Pyriglena) along the Atlantic Forest and the predictions derived from the river hypothesis and from a Last Glacial Maximum Pleistocene refuge paleomodel were compared to explain the patterns of genetic variation observed in these populations. A total of 266 individuals from 45 populations were sampled over a latitudinal transect and a number of phylogeographical and population genetics analytical approaches were employed to address these questions. The pattern of mtDNA variation observed in fire-eye antbirds provides little support for the view that populations were isolated by the modern course of major Atlantic Forest rivers. Instead, the data provide stronger support for the predictions of the refuge model. These results add to the mounting evidence that climatic oscillations appear to have played a substantial role in shaping the phylogeographical structure and possibly the diversification of many taxa in this region. However, the results also illustrate the potential for more complex climatic history and historical changes in the geographical distribution of Atlantic Forest than envisioned by the refuge model. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 900824.

Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland

Range expansions are extremely common, but have only recently begun to attract attention in terms of their genetic consequences. As populations expand, demes at the wave front experience strong genetic drift, which is expected to reduce genetic diversity and potentially cause ‘allele surfing’, where alleles may become fixed over a wide geographical area even if their effects are deleterious. Previous simulation models show that range expansions can generate very strong selective gradients on dispersal, reproduction, competition and immunity. To investigate the effects of range expansion on genetic diversity and adaptation, we studied the population genomics of the bank vole (Myodes glareolus) in Ireland. The bank vole was likely introduced in the late 1920s and is expanding its range at a rate of ~2.5 km/year. Using genotyping-by-sequencing, we genotyped 281 bank voles at 5979 SNP loci. Fourteen sample sites were arranged in three transects running from the introduction site to the wave front of the expansion. We found significant declines in genetic diversity along all three transects. However, there was no evidence that sites at the wave front had accumulated more deleterious mutations. We looked for outlier loci with strong correlations between allele frequency and distance from the introduction site, where the direction of correlation was the same in all three transects. Amongst these outliers, we found significant enrichment for genic SNPs, suggesting the action of selection. Candidates for selection included several genes with immunological functions and several genes that could influence behaviour.

Loss of heterozygosity induced by a chromosomal double-strand break

The repair of chromosomal double-strand breaks (DSBs) is necessary for genomic integrity in all organisms. Genetic consequences of misrepair include chromosomal loss, deletion, and duplication resulting in loss of heterozygosity (LOH), a common finding in human solid tumors. Although work with radiation-sensitive cell lines suggests that mammalian cells primarily rejoin DSBs by nonhomologous mechanisms, alternative mechanisms that are implicated in chromosomal LOH, such as allelic recombination, may also occur. We have examined chromosomal DSB repair between homologs in a gene targeted mammalian cell line at the retinoblastoma (Rb) locus. We have found that allelic recombinational repair occurs in mammalian cells and is increased at least two orders of magnitude by the induction of a chromosomal DSB. One consequence of allelic recombination is LOH at the Rb locus. Some of the repair events also resulted in other types of genetic instability, including deletions and duplications. We speculate that mammalian cells may have developed efficient nonhomologous DSB repair processes to bypass allelic recombination and the potential for reduction to homozygosity.

Population genetics of Ice Age brown bears

The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of glaciation, local extinctions, and intercontinental migration. The genetic consequences of these events are difficult to resolve from the study of present-day populations. To provide a direct view of population genetics in the late Pleistocene, we measured mitochondrial DNA sequence variation in seven permafrost-preserved brown bear (Ursus arctos) specimens, dated from 14,000 to 42,000 years ago. Approximately 36,000 years ago, the Beringian brown bear population had a higher genetic diversity than any extant North American population, but by 15,000 years ago genetic diversity appears similar to the modern day. The older, genetically diverse, Beringian population contained sequences from three clades now restricted to local regions within North America, indicating that current phylogeographic patterns may provide misleading data for evolutionary studies and conservation management. The late Pleistocene phylogeographic data also indicate possible colonization routes to areas south of the Cordilleran ice sheet.

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50-80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in F-ST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (F-ST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.

The effect of larval age on morphology and gene expression during ascidian metamorphosis

Metamorphosis is both an ecological and a developmental genetic transition that an organism undergoes as a normal part of ontogeny. Many organisms have the ability to delay metamorphosis when conditions are unsuitable. This strategy carries obvious benefits, but may also result in severe consequences for older larvae that run low on energy. In the marine environment, some lecithotrophic larvae that have prolonged periods in the plankton may begin forming postlarval and juvenile structures that normally do not appear until after settlement and the initiation of metamorphosis. This precocious activation of the postlarval developmental program may reflect an adaptation to increase the survival of older, energy-depleted larvae by allowing them to metamorphose more quickly. In the present study, we investigate morphological and genetic consequences of delay of metamorphosis in larvae of Herdmania momus (a solitary stolidobranch ascidian). We observe significant morphological and genetic changes during prolonged larval life, with older larvae displaying significant changes in RNA levels, precocious migration of mesenchyme cells, and changes in larval shape including shortening of the tail. While these observations suggest that the older H. momus larvae are functionally different from younger larvae and possibly becoming more predisposed to undergo metamorphosis, we did not find any significant differences in gene expression levels between postlarvae arising from larvae that metamorphosed as soon as they were competent and postlarvae developing from larvae that postponed metamorphosis. This recalibration, or convergence, of transcript levels in the early postlarva suggests that changes that occur during prolonged larval life of H. momus are not necessarily associated with early activation of adult organ differentiation. Instead, it suggests that an autonomous developmental program is activated in H. momus upon the induction of metamorphosis regardless of the history of the larva.

The relationship between vegetation and modern pollen assemblages on Mount Paggeo (NE Greece)

In this study, we investigated the relationship between vegetation and modern-pollen rain along the elevational gradient of Mount Paggeo. We apply multivariate data analysis to assess the relationship between vegetation and modern-pollen rain and quantify the representativeness of forest zones. This study represents the first statistical analysis of pollen-vegetation relationship along an elevational gradient in Greece. Hence, this paper improves confidence in interpretation of palynological records from north-eastern Greece and may refine past climate reconstructions for a more accurate comparison of data and modelling. Numerical classification and ordination were performed on pollen data to assess differences among plant communities that beech (Fagus sylvatica) dominates or co-dominates. The results show a strong relationship between altitude, arboreal cover, human impact and variations in pollen and nonpollen palynomorph taxa percentages.