Immigration dynamics of tropical and subtropical Southeast Asian limestone karst floras

Ex situ origins and dispersal of taxa have played important roles in the assembly of island-like biodiversity hotspots. Insular limestone karsts in Southeast Asia are hotspots of biodiversity and endemism, but the immigration processes of their unique floras are still poorly known. Here, we used Gesneriaceae as a proxy to investigate the immigration dynamics of tropical and subtropical Southeast Asian karst floras. We present the most comprehensive phylogenetic analysis of the Old World gesneriads to date based on twelve loci. By estimating divergence times and reconstructing ancestral states (habitat, soil type and range), we found that immigration into subtropical Southeast Asian karst floras first occurred in the Early Miocene, with two peaks in the Early–Middle Miocene and the Pliocene–Early Pleistocene, whereas immigration into tropical Southeast Asian karsts initiated in the Late Eocene, with two peaks in the Late Oligocene and the Late Miocene. We also discover that Southeast Asian karst biodiversity comprises immigrant pre-adapted lineages and descendants from local acid soil ancestors, although niche shift from acid soil to karst in tropical Southeast Asian islands was lacking. This study advances our understanding of the historical assembly of Southeast Asian karst floras.

Selection-driven adaptation to the extreme Antarctic environment in the Emperor penguin

The eco-evolutionary history of penguins is profoundly influenced by their shift from temperate to cold environments. Breeding only in Antarctica during the winter, the Emperor penguin appears as an extreme outcome of this process, with unique features related to insulation, heat production and energy management. However, whether this species actually diverged from a less cold-adapted ancestor, thus more similar in ecology to its sister species, the King penguin, is still an open question. As the Antarctic niche shift likely resulted in vast changes in selective pressure experienced by the Emperor penguin, the identification and relative quantification of the genomic signatures of selection, unique to each of these sister species, could answer this question. Applying a suite of phylogeny-based methods on 7,651 orthologous gene alignments of seven penguins and 13 other birds, we identified a set of candidate genes showing significantly different selection regimes either in the Emperor or in the King penguin lineage. Our comparative approach unveils a more pervasive selection shift in the Emperor penguin, supporting the hypothesis that its extreme cold adaptation is a derived state from a more King penguin-like ecology. Among the candidate genes under selection in the Emperor penguin, four genes (TRPM8, LEPR, CRB1, and SFI1) were identified before in other cold adapted vertebrates, while, on the other hand, 161 genes can be assigned to functional pathways relevant to cold adaptation (e.g., cardiovascular system, lipid, fatty acid and glucose metabolism, insulation, etc.). Our results show that extreme cold adaptation in the Emperor penguin largely involved unique genetic options which, however, affect metabolic and physiological traits common to other cold-adapted homeotherms.

Realised Niche Shifts, Rapid Evolution and Phenotypic Plasticity in Introduced Plants

<p>Recent biological invasions provide a unique opportunity to examine how species may adapt to novel conditions over relatively short time frames. Introduced species may respond to novel environmental conditions in the new range via rapid evolution, phenotypic plasticity, or the rapid evolution of phenotypic plasticity. However, the prevalence of these different mechanisms in introduced species remains unclear. In this thesis, I explore how introduced plant species may adjust their phenotype when introduced to a new range. First, I tested for evidence of phenotypic change through time in key morphological traits (plant height, leaf area, leaf shape, and leaf mass per unit area), using historic herbarium records for 34 plants introduced to Australia and New Zealand. Thirty-two out of 94 trait-species combinations showed evidence for change through time. The rate and direction of trait change was variable across species and the local climate. One possibility is that species introduced to a new range exhibit different trait responses depending on the relative difference in environment between the native and introduced range. To investigate this, I quantified climatic niche shifts in introduced species relative to their native range. I then predicted trait change through time from the magnitude and direction of climate niche shift in a meta-regression. This is the first study to simultaneously assess trait change in multiple introduced species in relation to a shift in their realised niche. Overall, climate niche shifts did not predict trait change through time, suggesting that climate may not be the predominant driver of trait change in plants introduced to Australia and New Zealand. Alternatively, the combined uncertainty and the mismatch in spatial scales that may arise when combining these two methods could mask any underlying patterns in plant trait responses to the new environment. It has been hypothesised that introduced species may respond to a sudden change in environment, by rapidly selecting for an increase in phenotypic plasticity. I tested for a difference in phenotypic plasticity between the native and introduced ranges of a beach daisy, Arctotheca populifolia. Contrary to my expectations, A. populifolia has shown a loss of phenotypic plasticity in as little as 80 years since its introduction to Australia. When using a meta-analysis to test for an overall difference in plasticity across multiple traits, I found that the current practice of calculating an effect size of an effect size (Hedges’ d) can lead to misleading results. I demonstrate how this issue arises when calculating a difference in Hedges’ d between two populations with different standard deviations. I propose an alternative way to calculate Hedges’ d to give a more accurate reflection of the difference in plasticity between ranges. Finally, I combine different lines of evidence from the previous chapters in a case study to explore how A. populifolia has changed since its introduction to Australia, and examine any discrepancies between the results. A glasshouse experiment revealed distinct trait differences between native and introduced populations of A. populifolia, which were not reflected in trait change through time inferred from herbarium specimens. Additionally, measured trait differences between ranges in the glasshouse experiment better reflected a niche shift into wetter climate, than the predicted trait change through time from herbarium specimens. This suggests that trait differences determined in glasshouse or common garden experiments, may be a more suitable approach to assess trait change in relation to a realised niche shift than using herbarium specimens.</p>

Realised Niche Shifts, Rapid Evolution and Phenotypic Plasticity in Introduced Plants

<p>Recent biological invasions provide a unique opportunity to examine how species may adapt to novel conditions over relatively short time frames. Introduced species may respond to novel environmental conditions in the new range via rapid evolution, phenotypic plasticity, or the rapid evolution of phenotypic plasticity. However, the prevalence of these different mechanisms in introduced species remains unclear. In this thesis, I explore how introduced plant species may adjust their phenotype when introduced to a new range. First, I tested for evidence of phenotypic change through time in key morphological traits (plant height, leaf area, leaf shape, and leaf mass per unit area), using historic herbarium records for 34 plants introduced to Australia and New Zealand. Thirty-two out of 94 trait-species combinations showed evidence for change through time. The rate and direction of trait change was variable across species and the local climate. One possibility is that species introduced to a new range exhibit different trait responses depending on the relative difference in environment between the native and introduced range. To investigate this, I quantified climatic niche shifts in introduced species relative to their native range. I then predicted trait change through time from the magnitude and direction of climate niche shift in a meta-regression. This is the first study to simultaneously assess trait change in multiple introduced species in relation to a shift in their realised niche. Overall, climate niche shifts did not predict trait change through time, suggesting that climate may not be the predominant driver of trait change in plants introduced to Australia and New Zealand. Alternatively, the combined uncertainty and the mismatch in spatial scales that may arise when combining these two methods could mask any underlying patterns in plant trait responses to the new environment. It has been hypothesised that introduced species may respond to a sudden change in environment, by rapidly selecting for an increase in phenotypic plasticity. I tested for a difference in phenotypic plasticity between the native and introduced ranges of a beach daisy, Arctotheca populifolia. Contrary to my expectations, A. populifolia has shown a loss of phenotypic plasticity in as little as 80 years since its introduction to Australia. When using a meta-analysis to test for an overall difference in plasticity across multiple traits, I found that the current practice of calculating an effect size of an effect size (Hedges’ d) can lead to misleading results. I demonstrate how this issue arises when calculating a difference in Hedges’ d between two populations with different standard deviations. I propose an alternative way to calculate Hedges’ d to give a more accurate reflection of the difference in plasticity between ranges. Finally, I combine different lines of evidence from the previous chapters in a case study to explore how A. populifolia has changed since its introduction to Australia, and examine any discrepancies between the results. A glasshouse experiment revealed distinct trait differences between native and introduced populations of A. populifolia, which were not reflected in trait change through time inferred from herbarium specimens. Additionally, measured trait differences between ranges in the glasshouse experiment better reflected a niche shift into wetter climate, than the predicted trait change through time from herbarium specimens. This suggests that trait differences determined in glasshouse or common garden experiments, may be a more suitable approach to assess trait change in relation to a realised niche shift than using herbarium specimens.</p>

Factors Promoting Coexistence between Endemic Ants and Invasive Wasps

<p>Invasive animals can alter the community composition of native ecosystems by means of competition and predation. In this study I investigated the factors that may facilitate coexistence between endemic ants and invasive wasps. Previous research has shown that entire communities can be impacted by invasions. Endemic species subject to pressure from invasive species may undergo a niche shift to enable coexistence and minimise the impact of this pressure. The invertebrate community composition of Nothofagus forests in the South Island of New Zealand has been altered by predation from Invasive Vespula wasps. Ants and wasps in this ecosystem coexist on the same trophic level; they simultaneously fill multiple trophic roles as primary predators, secondary predators, and primary consumers. The outcome of competition between species such as ants and wasps is not easy to predict, and may vary in different communities and with different densities of competitors. In this dissertation I aimed to determine the extent to which competition occurs between native ants and invasive Vespula wasps, and to investigate the impacts of invasion on the native invertebrate community. I quantified the invertebrate community composition of Nothofagus forests and then experimentally reduced wasp numbers to investigate any changes as a result of a reduction in predation or competition. The observed changes in community composition were as a result of differing abundances of taxonomic groups within my study sites. In order to more robustly determine the community effects of wasp removal it may be necessary to reduce wasp numbers by up to 90% for many years. Even under these conditions, species that are particularly vulnerable to wasp predation or competition may have already been permanently excluded from this system. I then investigated temporal niche shifts by native ants when faced with reduced competition for food resources from invasive wasps. There was an increase in the numbers of ants foraging on honeydew when I experimentally reduced wasp numbers. This increase may be due to increases in both the quantity and quality of the available honeydew. When densities of wasps were substantially reduced there was a difference in the foraging abundances of ants and wasps; however, there was no change in the overall temporal foraging pattern of ants. Isotope ratios and consequently trophic levels of native competitors may change in response to the removal of an invasive species. To test this I examined changes in isotope ratios as a result of removal of wasps. The observed changes in the trophic levels of both ants and wasps appear to be a result of natural seasonal variation in consumption related to the nutritional requirements of the colony. Finally, I examined behavioral interactions between native ants and invasive wasps during foraging. This study has indicated that wasps may find and access resources more readily when ants are present. Native ants may facilitate foraging by wasps, as demonstrated by the increase in wasp numbers when foraging in the presence of ants. Additionally, the impact of competition between wasps and ants is likely to be density dependant. Co-occurrence between endemic and invasive competitors is possible through two important mechanisms, niche separation and behavioural adaptations. Native ants in this system are able to forage in different temporal niches than invasive wasps, and their dominant behaviour serves to diminish competitive interactions. These findings have implications for the ecology of these forests in understanding the considerable impact that invasive species may have on native ecosystems and particularly those species which have similar resource requirements.</p>

Factors Promoting Coexistence between Endemic Ants and Invasive Wasps

<p>Invasive animals can alter the community composition of native ecosystems by means of competition and predation. In this study I investigated the factors that may facilitate coexistence between endemic ants and invasive wasps. Previous research has shown that entire communities can be impacted by invasions. Endemic species subject to pressure from invasive species may undergo a niche shift to enable coexistence and minimise the impact of this pressure. The invertebrate community composition of Nothofagus forests in the South Island of New Zealand has been altered by predation from Invasive Vespula wasps. Ants and wasps in this ecosystem coexist on the same trophic level; they simultaneously fill multiple trophic roles as primary predators, secondary predators, and primary consumers. The outcome of competition between species such as ants and wasps is not easy to predict, and may vary in different communities and with different densities of competitors. In this dissertation I aimed to determine the extent to which competition occurs between native ants and invasive Vespula wasps, and to investigate the impacts of invasion on the native invertebrate community. I quantified the invertebrate community composition of Nothofagus forests and then experimentally reduced wasp numbers to investigate any changes as a result of a reduction in predation or competition. The observed changes in community composition were as a result of differing abundances of taxonomic groups within my study sites. In order to more robustly determine the community effects of wasp removal it may be necessary to reduce wasp numbers by up to 90% for many years. Even under these conditions, species that are particularly vulnerable to wasp predation or competition may have already been permanently excluded from this system. I then investigated temporal niche shifts by native ants when faced with reduced competition for food resources from invasive wasps. There was an increase in the numbers of ants foraging on honeydew when I experimentally reduced wasp numbers. This increase may be due to increases in both the quantity and quality of the available honeydew. When densities of wasps were substantially reduced there was a difference in the foraging abundances of ants and wasps; however, there was no change in the overall temporal foraging pattern of ants. Isotope ratios and consequently trophic levels of native competitors may change in response to the removal of an invasive species. To test this I examined changes in isotope ratios as a result of removal of wasps. The observed changes in the trophic levels of both ants and wasps appear to be a result of natural seasonal variation in consumption related to the nutritional requirements of the colony. Finally, I examined behavioral interactions between native ants and invasive wasps during foraging. This study has indicated that wasps may find and access resources more readily when ants are present. Native ants may facilitate foraging by wasps, as demonstrated by the increase in wasp numbers when foraging in the presence of ants. Additionally, the impact of competition between wasps and ants is likely to be density dependant. Co-occurrence between endemic and invasive competitors is possible through two important mechanisms, niche separation and behavioural adaptations. Native ants in this system are able to forage in different temporal niches than invasive wasps, and their dominant behaviour serves to diminish competitive interactions. These findings have implications for the ecology of these forests in understanding the considerable impact that invasive species may have on native ecosystems and particularly those species which have similar resource requirements.</p>

Trophic Ecology of Juvenile Southern King Crab Associated with Kelp Forest: Evidence of Cannibalism

The southern king crab, Lithodes santolla, is a well-known predator/scavenger species during its adult phase but its feeding strategy in early stages is less studied. This information is important to understand their role in ecosystems and to improve fishery management (i.e., stock enhancement). Based on stomach contents and stable isotope analysis, we determined variation in the composition of diet and niche overlap in vagile and cryptic phase collected within and outside a kelp forest, Macrocystis pyrifera, of Aguila Bay at the Magellan Strait in Patagonia, Chile. Results of juvenile stomach content analysis showed 60% dissimilarity between cryptic and vagile juvenile phases. Algae dominated the volumetric contribution in cryptic juveniles while crustacean dominated the diet in vagile phase. Exoskeleton of other king crabs occurred in 43% of juveniles with crustaceans in their stomach. This fact confirms cannibalistic behavior in the wild in this species, which is consistent with findings in massive laboratory cultures. There was no evidence of isotopic niche shift between cryptic and vagile juvenile phases. Overlapping isotopic niches of different-sized juveniles suggest that they exploit similar food resources. However, vagile individuals occupy a higher trophic position than cryptic individuals, which could suggest a switch in dietary preference, from detritivorous/herbivory within kelp forests to omnivory outside of kelp forests, and an increase in the level of cannibalism in vagile juveniles.

Species Distribution Models of the Spartina alterniflora Loisel in Its Origin and Invasive Country Reveal an Ecological Niche Shift

Spartina alterniflora is a perennial herb native to the American Atlantic coast and is the dominant plant in coastal intertidal wetlands. Since its introduction to China in 1979, it has quickly spread along the coast and has caused various hazards. To control the further spread of S. alterniflora in China, we first reconstructed the history of the spread of S. alterniflora in its invasion and origin countries. We found that S. alterniflora spreads from the central coast to both sides of the coast in China, while it spreads from the west coast to the east coast in America. Furthermore, by comparing 19 environmental variables of S. alterniflora in its invasion and origin countries, it was found that S. alterniflora is more and more adaptable to the high temperature and dry environment in the invasion country. Finally, we predicted the suitable areas for this species in China and America using the maximum entropy (MaxEnt) model and ArcGIS. Overall, through analysis on the dynamic and trend of environmental characteristics during the invasion of S. alterniflora and predicting its suitable area in the invasion area, it guides preventing its reintroduction and preventing its further spread of the species has been found. It has reference significance for studying other similar alien plants and essential enlightening relevance to its invasion and spread in similar areas.

Global Assessment of Climatic Niche Shifts in Three Rumex Species

Climatic niche shifts occur when species occupy different climates in the introduced range than in their native range. We know that climatic niche shifts are common occurrences, however we do not currently understand whether climatic niche shifts can consistently be predicted across the globe. Using three congeneric weed species, we investigate whether the known presence of a climatic niche shift in one range can help predict a species’ distribution in other ranges. We consider whether data either from other ranges or from closely related species can help predict whether climatic niche shifts will occur. We compared the climatic conditions occupied by Rumex obtusifolius, R. crispus, and R. conglomeratus between their native range (Eurasia) and three different introduced ranges (North America, Australia, New Zealand). We consider metrics of niche overlap, expansion, unfilling, pioneering, and similarity to determine whether i) climatic niche shifts have occurred and ii) climatic niche shifts were consistent across ranges and congeners. We found that the presence and direction of climatic niche shifts is inconsistent across ranges for all three species. Within an introduced range, however, niche shifts were similar between species. Despite this, species distributions outside of their native range could not be reliably predicted by the distributions of congeners in either their native or introduced ranges. This study is the first of its kind to consider niche shifts across multiple introduced ranges and species, highlighting new challenges in predicting species distributions when species undergo climatic niche shifts.

Evidence of a trophic niche shift in an omnivorous migratory bird in South America: A comparison of stable isotope signatures in feathers between migratory and sedentary subspecies of Tyrannus savana

Understanding how diet and life history strategies interact is important for exploring constraints of available nutrition on energetically expensive life history events in wild animals (i.e., reproduction, annual migration, or molt). Previous research on migratory birds breeding in the Northern Hemisphere has demonstrated trophic niche shifts from invertebrates to fruit in order to fuel spring migration. We examined whether a trophic niche switch occurred in a Neotropical austral migrant bird, Tyrannus savana savana prior to spring migration by measuring stable nitrogen isotopes in feathers. We found that the austral migrant T. s. savana did appear to shift in diet from a higher to lower trophic level (consistent in pattern with a shift from a higher to lower ratio of invertebrates to fruit) but the shift occurred earlier than expected if it was preparation for migration. A sympatric sedentary subspecies (T. s. monachus) appeared to forage only at the lower trophic level during their annual molt and that show no evidence of a trophic niche shift. The timing of the trophic niche shift leads us to conclude that a higher trophic level diet early in molt is not related to preparation for spring migration in this species but suggest that it may be related to seasonal changes in food availability as the wet season concludes. A remaining challenge for understanding the ecological consequences of trophic niche shifts is to find ways to empirically measure trade-offs between different diets across energetically expensive life history activities and compare these between taxa with differing life history strategies.