Climatic niche conservatism in a clade of disease vectors (Diptera: Phlebotominae)

Sandflies of the family Psychodidae show notable diversity in both disease vector status and climatic niche. Some species (in the subfamily Phlebotominae) transmit Leishmania parasites, responsible for the disease leishmaniasis. Other Psychodidae species do not. Psychodid species ranges can be solely tropical, confined to the temperate zones, or span both. Studying the relationship between the evolution of disease vector status and that of climatic niche affords an understanding not only of the climate conditions associated with the presence and species richness of Leishmania vectors, but also allows the study of the extent to which the climatic niches of psychodid flies are conserved, in a context with implications for global human health. We obtained observation site data, and associated climate data, for 223 psychodid species to understand which aspects of climate most closely predict distribution. Temperature and seasonality are strong determinants of species occurrence within the clade. We built a mitochondrial DNA phylogeny of Psychodidae, and found a positive relationship between pairwise genetic distance and climate niche differentiation, which indicates strong niche conservatism. This result is also supported by strong phylogenetic signals of metrics of climate differentiation. Finally, we used ancestral trait reconstruction to infer the tropicality (i.e., proportion of latitudinal range in the tropics minus the proportion of the latitudinal range in temperate areas) of ancestral species, and counted transitions to and from tropicality states, finding that tropical and temperate species respectively produced almost entirely tropical and temperate descendant species, a result consistent for vector and non-vector species. Taken together, these results imply that while vectors of Leishmania can survive in a variety of climates, their climate niches are strongly predicted by phylogeny.

Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation

Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host’s ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.

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>

Niche Shifts, Hybridization, Polyploidy and Geographic Parthenogenesis in Western North American Hawthorns (Crataegus subg. Sanguineae, Rosaceae)

We compare biogeographic and morphological parameters of two agamic complexes of western North American hawthorns so as to evaluate possible explanations of the differences in range between sexually reproducing taxa and their apomictic sister taxa. We have documented range, breeding system, morphology, leaf vascular architecture, and niche breadth in these hawthorns, for which phylogenetic relationships and ploidy levels are known. Species distribution data from herbarium specimens and online databases were analyzed in order to compare ranges and climate niches described by bioclimatic variables. Flow cytometry documented ploidy level and breeding system. Voucher specimens provided morphometric data that were analyzed using uni- and multivariate methods. Members of two black-fruited taxonomic sections of Crataegus subg. Sanguineae (sections Douglasianae, Salignae) have previously been identified as hybrids. They are presumptively self-fertile polyploids with pseudogamous gametophytic apomixis. Their morphologies, geographic ranges, and niche characteristics resemble those of their diploid, sexual parent or are intermediate between them and those of their other parent, one or both of two partially sympatric tetraploid apomicts in red-fruited C. subg. Americanae with much wider distributions. Comparing sections Douglasianae and Salignae suggests that geographic parthenogenesis (larger range sizes in apomicts, compared to sexually reproducing taxa) may have less to do with adaptation than it does with reproductive assurance in the pseudogamously apomictic and self-compatible hybrids. Greater climate niche breadth in allopolyploids compared to diploids similarly may be more due to parental traits than to effects of genome duplication per se.

Where Do the World’s Squirrel Hotspots and Coldspots of 230+ Species Go with Climate Change 2100? A First BIG DATA Minimum Estimate from an Open Access Climate Niche Rapid Model Assessment

Man-made climate change and its impact on the living world remain the problem of our time waiting for a good science-based resolution. Here, we focus on forecasting the global squirrel population as a representative but overlooked species group for the year 2100. This was possible by using 230 publicly available Species Distribution Model prediction maps for the world’s squirrels (233 out of 307; 75%). These distribution forecasts are originating from 132 GIS predictors, implemented with an ensemble of three machine learning algorithms (TreeNet, RandomForest, and Maxent). We found that most of the world’s squirrel ranges will be shifting (usually towards higher altitudes and latitudes) and remain/ become more fragmented; some species extend their range, and many can ‘spill’ into new landscapes. Considering that here we just ran a Rapid Assessment of Big Data, dealing with a climate niche envelope of the future but not the entire more holistic perspective of climate change and 2100, we assume wider serious changes will occur for squirrels, their habitats, and the world in the future Anthropocene of 2100. These changes can lead to more stress, genetic loss, extinction, and increased zoonotic disease transmissions, and this process will occur with an increased gradient over time.

Drivers of an epic radiation: the role of climate and islands in species diversification and reproductive-mode evolution of Old-World tree frogs

Although large diversifications of species occur unevenly across space and evolutionary lineages, the relative importance of their driving mechanisms, such as climate, ecological opportunity and key innovations, remains poorly understood. Here, we explore the remarkable diversification of rhacophorid frogs, which represent six percent of global amphibian diversity, utilize four distinct reproductive modes, and span a climatically variable area across mainland Asia, associated continental islands, and Africa. Using a complete species-level phylogeny, we find near-constant diversification rates but a highly uneven distribution of species richness. Montane regions on islands and some mainland regions have higher phylogenetic diversity and unique assemblages of taxa; we identify these as cool-wet refugia. Starting from a centre of origin, rhacophorids reached these distant refugia by adapting to new climatic conditions (niche evolution-dominant), especially following the origin of key innovations such as terrestrial reproduction (in the Late Eocene) or by dispersal during periods of favourable climate (niche conservatism-dominant).

Global Patterns of the Fungal Pathogen Batrachochytrium dendrobatidis Support Conservation Urgency

The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) is a skin pathogen that can cause the emerging infectious disease chytridiomycosis in susceptible species. It has been considered one of the most severe threats to amphibian biodiversity. We aimed to provide an updated compilation of global Bd occurrences by host taxon and geography, and with the larger global Bd dataset we reanalyzed Bd associations with environmental metrics at the world and regional scales. We also compared our Bd data compilation with a recent independent assessment to provide a more comprehensive count of species and countries with Bd occurrences. Bd has been detected in 1,375 of 2,525 (55%) species sampled, more than doubling known species infections since 2013. Bd occurrence is known from 93 of 134 (69%) countries at this writing; this compares to known occurrences in 56 of 82 (68%) countries in 2013. Climate-niche space is highly associated with Bd detection, with different climate metrics emerging as key predictors of Bd occurrence at regional scales; this warrants further assessment relative to climate-change projections. The accretion of Bd occurrence reports points to the common aims of worldwide investigators to understand the conservation concerns for amphibian biodiversity in the face of potential disease threat. Renewed calls for better mitigation of amphibian disease threats resonate across continents with amphibians, especially outside Asia. As Bd appears to be able to infect about half of amphibian taxa and sites, there is considerable room for biosecurity actions to forestall its spread using both bottom-up community-run efforts and top-down national-to-international policies. Conservation safeguards for sensitive species and biodiversity refugia are continuing priorities.

Transposable elements in the genome of the lichen-forming fungus Umbilicaria pustulata, and their distribution in different climate zones along elevation

Background: Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance. Results: We found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. Conclusions: This pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.