Evolutionary biology by Rutger Vos
biorxiv, 2019
The domestication of flora and fauna is one of the most significant transitions in humankind's hi... more The domestication of flora and fauna is one of the most significant transitions in humankind's history. It changed human societies drastically with alterations in biodiversity, atmospheric composition and land use. Humans have domesticated relatively few large animals and all of them belong to the Ungu-lates, though they are only 15 species of the ±150 that the entire group comprises. This can partially be explained by behav-ioral and life history pre-adaptations, e.g. social group structure , mating behavior, parent-young interaction, feeding behavior , and response to humans. The other dimension of proposed pre-adapatations concerns the biomes from which domesticated Ungulates originate. Here we test whether environmental preferences i.e. niches and related niche traits, differentiate between wild and domesticated Ungulates. We used three methods to determine the niche dimensions for each species and calculate overlap in niche space between them. Two methods are based on MaxEnt ecological niche models and one method uses raw occurrence data. Our results show that there is no weighted combination of environmental traits that clusters all domesticated Ungulates to the exclusion of all wild ones. On the contrary , domesticated Ungulates are overdispersed in niche space, indicating that the major pre-adaptations for domestication are not directly related to the abiotic niche. However, phylogenetic generalized linear modelling of selected niche dimensions does predict domestication significantly. We conclude that further research of other traits is needed.
bioRxiv, 2019
Knowledge of global biodiversity remains limited by geographic and taxonomic sampling biases. The... more Knowledge of global biodiversity remains limited by geographic and taxonomic sampling biases. The scarcity of species data restricts our understanding of the underlying environmental factors shaping distributions, and the ability to draw comparisons among species. Species distribution models (SDMs) were developed in the early 2000s to address this issue. Although SDMs based on single layered Neural Networks have been experimented with in the past, these performed poorly. However, the past two decades have seen a strong increase in the use of Deep Learning (DL) approaches, such as Deep Neural Networks (DNNs). Despite the large improvement in predictive capacity DNNs provide over shallow networks, to our knowledge these have not yet been applied to SDM. The aim of this research was to provide a proof of concept of a DL-SDM 1. We used a pre-existing dataset of the world's ungulates and abiotic environmental predictors that had recently been used in MaxEnt SDM, to allow for a direct comparison of performance between both methods. Our DL-SDM consisted of a binary classification DNN containing 4 hidden layers and drop-out regularization between each layer. Performance of the DL-SDM was similar to MaxEnt for species with relatively large sample sizes and worse for species with relatively low sample sizes. Increasing the number of occurrences further improved DL-SDM performance for species that already had relatively high sample sizes. We then tried to further improve performance by altering the sampling procedure of negative instances and increasing the number of environmental predictors, including species interactions. This led to a large increase in model performance across the range of sample sizes in the species datasets. We conclude that DL-SDMs provide a suitable alternative to traditional SDMs such as MaxEnt and have the advantage of being both able to directly include species interactions, as well as being able to handle correlated input features. Further improvements to the model would include increasing its scalability by turning it into a multi-classification model, as well as developing a more user friendly DL-SDM Python package.
biorxiv, 2019
Understanding what interactions and environmental factors shape the geographic distribution of sp... more Understanding what interactions and environmental factors shape the geographic distribution of species is one of the fundamental questions in ecology and evolution. Insofar as the focus is on agriculturally important species, insight into this is also of applied importance. Species Distribution Modeling (SDM) comprises a spectrum of approaches for establishing correlative models of species (co-)occurrences and geospatial patterns of abiotic environmental variables. Here, we contribute to this field by presenting a generalized approach for SDM that utilizes deep learning, which offers some improvements over current methods, and by presenting a case study on the habitat suitability of staple crops and their wild ancestors. The approach we present is implemented in a reusable software toolkit, which we apply to an extensive data set of geo-referenced occurrence records for 52 species and 59 GIS layers. We compare the habitat suitability projections for selected, major crop species with the actual extent of their current cultivation. Our results show that the approach yields especially plausible projections for species with large numbers of occurrences (>500). For the analysis of such data sets, the toolkit provides a convenient interface for using deep neural networks in SDM, a relatively novel application of deep learning. The toolkit, the data, and the results are available as open source / open access packages. Species Distribution Modeling with deep learning is a promising avenue for method development. The niche projections that can be produced are plausible, and the general approach provides great flexibility for incorporating additional data such as species interactions.
Scientific Reports, 2018
Mycorrhizal symbiosis between soil fungi and land plants is one of the most widespread and ecolog... more Mycorrhizal symbiosis between soil fungi and land plants is one of the most widespread and ecologically important mutualisms on earth. It has long been hypothesized that the Glomeromycotina, the mycorrhizal symbionts of the majority of plants, facilitated colonization of land by plants in the Ordovician. This view was recently challenged by the discovery of mycorrhiza-like associations with Mucoromycotina in several early diverging lineages of land plants. Utilizing a large, species-level database of plants’ mycorrhiza-like associations and a Bayesian approach to state transition dynamics we here show that the recruitment of Mucoromycotina is the best supported transition from a non-mycorrhizal state. We further found that transitions between different combinations of either or both of Mucoromycotina and Glomeromycotina occur at high rates, and found similar promiscuity among combinations that include either or both of Glomeromycotina and Ascomycota with a nearly fixed association with Basidiomycota. Our results portray an evolutionary scenario of evolution of mycorrhizal symbiosis with a prominent role for Mucoromycotina in the early stages of land plant diversification.
American Journal of Botany, 2018
Providing science and society with an integrated, up‐to‐date, high quality, open, reproducible an... more Providing science and society with an integrated, up‐to‐date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree‐building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non‐experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re‐run at regular intervals, storing trees and their metadata long‐term. Providing the trees to a diverse global audience through user‐friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.
Journal of Insect Conservation, 2017
In drawing up Red Lists, the extinction risks of butterflies and other insects are currently asse... more In drawing up Red Lists, the extinction risks of butterflies and other insects are currently assessed mainly by using information on trends in distribution and abundance. Incorporating information on species traits may increase our ability to predict species responses to environmental change and, hence, their vulnerability. We summarized ecologically relevant life-history and climatic niche traits in principal components, and used these to explain the variation in five vulnerability indicators (Red List status, Endemicity, Range size, Habitat specialisation index, Affinity for natural habitats) for 397 European butterfly species out of 482 species present in Europe. We also evaluated a selection of 238 species to test whether phylogenetic correction affected these relationships. For all but the affinity for natural habitats, climatic niche traits predicted more variation in vulnerability than life-history traits; phylogenetic correction had no relevant influence on the findings. The life-history trait component reflecting mobility, development rate, and overwintering stage, proved the major non-climatic determinant of species vulnerability. We propose that this trait component offers a preferable alternative to the frequently used, but ecologically confusing generalist-specialist continuum. Our analysis contributes to the development of trait-based approaches to prioritise vulnerable species for conservation at a European scale. Further regional scale analyses are recommended to improve our understanding of the biological basis of species vulnerability.
Global Change Biology, 2017
Given the global continuous rise, artificial light at night is often considered a driving force b... more Given the global continuous rise, artificial light at night is often considered a driving force behind moth population declines. Although negative effects on individuals have been shown, there is no evidence for effects on population sizes to date. Therefore, we compared population trends of Dutch macromoth fauna over the period 1985–2015 between moth species that differ in phototaxis and adult circadian rhythm. We found that moth species that show positive phototaxis or are nocturnally active have stronger negative population trends than species that are not attracted to light or are diurnal species. Our results indicate that artificial light at night is an important factor in explaining declines in moth populations in regions with high artificial night sky brightness. Our study supports efforts to reduce the impacts of artificial light at night by promoting lamps that do not attract insects and reduce overall levels of illumination in rural areas to reverse declines of moth populations.
BMC Evolutionary Biology, 2017
Background: Thousands of flowering plant species attract pollinators without offering rewards, bu... more Background: Thousands of flowering plant species attract pollinators without offering rewards, but the evolution of this deceit is poorly understood. Rewardless flowers of the orchid Erycina pusilla have an enlarged median sepal and incised median petal ('lip') to attract oil-collecting bees. These bees also forage on similar looking but rewarding Malpighiaceae flowers that have five unequally sized petals and gland-carrying sepals. The lip of E. pusilla has a 'callus' that, together with winged 'stelidia', mimics these glands. Different hypotheses exist about the evolutionary origin of the median sepal, callus and stelidia of orchid flowers.
Annals of Botany, 2016
Angiosperms with simple vessel perforations have evolved many times independently of species havi... more Angiosperms with simple vessel perforations have evolved many times independently of species having scalariform perforations, but detailed studies to understand why these transitions in wood evolution have happened are lacking. We focus on the striking difference in wood anatomy between two closely related gen-era of Adoxaceae, Viburnum and Sambucus, and link the anatomical divergence with climatic and physiological insights. After performing wood anatomical observations, we used a molecular phylogenetic framework to estimate divergence times for 127 Adoxaceae species. The conditions under which the genera diversified were estimated using ancestral area reconstruction and optimization of ancestral climates, and xylem-specific conductivity measurements were performed. Viburnum, characterized by scalariform vessel perforations (ancestral), diversified earlier than Sambucus, having simple perforations (derived). Ancestral climate reconstruction analyses point to cold temperate preference for Viburnum and warm temperate for Sambucus. This is reflected in the xylem-specific conductivity rates of the co-occurring species investigated, showing that Viburnum lantana has rates much lower than Sambucus nigra. The lack of selective pressure for high conductive efficiency during early diversification of Viburnum and the potentially adaptive value of scalariform perforations in frost-prone cold temperate climates have led to retention of the ancestral vessel perforation type, while higher temperatures during early diversification of Sambucus have triggered the evolution of simple vessel perforations, allowing more efficient long-distance water transport.
Diversity and Distributions, 2016
Aim
To analyse the underpinnings of historical drivers of diversity and their contributions to cu... more Aim
To analyse the underpinnings of historical drivers of diversity and their contributions to current distributions and future roles in a changing climate, we studied the relationship between ecological niche divergence and phylogenetic signal in tropical carnivorous pitcher plants.
Location
Southeast Asia.
Methods
Estimates of realized ecological niches were reconstructed and plotted along a newly created multilocus molecular phylogeny. Phylogenetic signal was analysed by comparisons of calculated phylogenetic relatedness with ecological niche divergence. Current and projected future potentially suitable habitats were mapped for several species of plants with variable evolutionary histories and distributions.
Results
Highland and lowland species had distinct phylogenetic signals. Higher altitude species had significantly lower molecular divergence as compared with the lowland species, yet ecological niches with less overlap. When projected onto a future climate scenario, highland species lose a greater amount of potentially suitable habitat compared to lower altitude species, and the majority of studied higher altitude species will face an overall loss of future suitable habitat.
Main conclusion
We conclude that distinct phylogenetic signals not only unravel differing evolutionary histories but also show that the implications of species' tolerances to future changing climate vary. Over the past million years, historical climate change shaped the differing evolution and ecological niches of highland and lowland tropical pitcher plant species. Rapid, recent radiations of the higher altitude species are reflected in limited molecular divergence, which is in sharp contrast with the more gradually evolved and genetically distinct lower altitude species in our study. Our projections for future potentially suitable habitats show that on‐going climate shifts will have detrimental effects on especially the higher altitude species due to a narrower niche tolerance and dramatic loss of potentially suitable habitat.
PeerJ, 2016
The integration of invasive species into native food webs represent multifarious dynamics of ecol... more The integration of invasive species into native food webs represent multifarious dynamics of ecological and evolutionary processes. We document incorporation of Prunus serotina (black cherry) into native insect food webs. We find that P. serotina harbours a herbivore community less dense but more diverse than its native relative, P. padus (bird cherry), with similar proportions of specialists and generalists. While herbivory on P. padus remained stable over the past century, that on P. serotina gradually doubled. We show that P. serotina may have evolved changes in investment in cyanogenic glycosides compared with its native range. In the leaf beetle Gonioctena quinquepunctata, recently shifted from native Sorbus aucuparia to P. serotina, we find divergent host preferences on Sorbus- versus Prunus-derived populations, and weak host-specific differentiation among 380 individuals genotyped for 119 SNP loci. We conclude that evolutionary processes may generate a specialized herbivore community on an invasive plant, allowing prognoses of reduced invasiveness over time. On the basis of the results presented here, we would like to caution that manual control might have the adverse effect of a slowing down of processes of adaptation, and a delay in the decline of the invasive character of P. serotina.
BMC Evolutionary Biology, 2010
Background
Nutrition and predation have been considered two primary agents of selection important... more Background
Nutrition and predation have been considered two primary agents of selection important in the evolution of avian life history traits. The relative importance of these natural selective forces in the evolution of avian embryonic developmental period (EDP) remain poorly resolved, perhaps in part because research has tended to focus on a single, high taxonomic-level group of birds: Order Passeriformes. The marine bird families Alcidae (auks) and Spheniscidae (penguins) exhibit marked variation in EDP, as well as behavioural and ecological traits ultimately linked to EDP. Therefore, auks and penguins provide a unique opportunity to assess the natural selective basis of variation in a key life-history trait at a low taxonomic-level. We used phylogenetic comparative methods to investigate the relative importance of behavioural and ecological factors related to nutrition and predation in the evolution of avian EDP.
Results
Three behavioural and ecological variables related to nutrition and predation risk (i.e., clutch size, activity pattern, and nesting habits) were significant predictors of residual variation in auk and penguin EDP based on models predicting EDP from egg mass. Species with larger clutch sizes, diurnal activity patterns, and open nests had significantly shorter EDPs. Further, EDP was found to be longer among birds which forage in distant offshore waters, relative to those that foraged in near shore waters, in line with our predictions, but not significantly so.
Conclusion
Current debate has emphasized predation as the primary agent of selection driving avian life history diversification. Our results suggest that both nutrition and predation have been important selective forces in the evolution of auk and penguin EDP, and highlight the importance of considering these questions at lower taxonomic scales. We suggest that further comparative studies on lower taxonomic-level groups will continue to constructively inform the debate on evolutionary determinants of avian EDP, as well as other life history parameters.
Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the ... more Did the end-Cretaceous mass extinction event, by eliminating non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse a species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net per-lineage diversification rates barely changed across the Cretaceous/Tertiary boundary. Instead, these rates spiked significantly with the origins of the currently recognized placental superorders and orders approximately 93 million years ago, before falling and remaining low until accelerating again throughout the Eocene and Oligocene epochs. Our results show that the phylogenetic 'fuses' leading to the explosion of extant placental orders are not only very much longer than suspected previously, but also challenge the hypothesis that the end-Cretaceous mass extinction event had a major, direct influence on the diversification of today's mammals.
Nature, Jan 1, 2007
Did the end-Cretaceous mass extinction, by wiping out non-avian dinosaurs and most of the existin... more Did the end-Cretaceous mass extinction, by wiping out non-avian dinosaurs and most of the existing fauna, trigger the evolutionary radiation of present-day mammals? Here we construct, date and analyse the first species-level phylogeny of nearly all extant Mammalia to bring a new perspective to this question. Our analyses of how extant lineages accumulated through time show that net perlineage diversification rates barely change across the Cretaceous-Tertiary boundary. Instead, rates spike significantly with the origins of the currently
European Journal of …, Jan 1, 2006
To understand the evolution of insect gut symbionts it is important to determine how they are pas... more To understand the evolution of insect gut symbionts it is important to determine how they are passed on to the next generation. We studied this process in Erwinia species bacteria that inhabit the gut of western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae). This is a polyphagous herbivore and a world-wide pest in agricultural crops. With bacteria in the gut, the thrips larval development time can be shorter and its oviposition rate higher compared to bacteria-free thrips. Bacteria are not directly transmitted from mother to offspring, but larvae acquire bacteria from the leaves right after they hatch. These gut bacteria are present on the leaves on feeding sites used by other thrips before the larvae arrive, probably because these other thrips have deposited bacteria via faeces or regurgitation. In this study we addressed the question whether the transmission route of symbiotic bacteria influences the thrips feeding behaviour, and determined the feeding and oviposition preference of thrips, by giving them a choice between leaves with and leaves without prior grazing by other western flower thrips. This was studied for thrips with and thrips without gut bacteria. Young larvae prefer to feed on leaves that where grazed before by other thrips and females prefer to oviposit on these grazed leaves. These results are in contradiction to earlier studies that have found that thrips larvae fitness is lower on thrips damaged plants than on clean plants. This behaviour does however promote the establishment of gut bacteria in the thrips. The factors determining the preference for thrips-damaged leaves may be the physical leaf damage or odours that are produced by the plant, the bacteria or both.
Journal of Evolutionary Biology, Dec 20, 2001
Studies of the genetics of speciation are fundamental to our understanding of its causes and cons... more Studies of the genetics of speciation are fundamental to our understanding of its causes and consequences. A tacit assumption of speciation research is that species are real evolutionary units. Different species concepts place different emphases on properties of species and so have the potential to shift the focus of studies of speciation. At present, the genetics of speciation is effectively the genetics of reproductive isolation (Coyne & Orr, 1998). In this vein, Wu et al. have been at the forefront of endeavours to understand the ...
Bioinformatics by Rutger Vos
The Journal of Open Source Software, 2019
The process of submitting annotated genomes to NCBI GenBank - and having them pass review - is a ... more The process of submitting annotated genomes to NCBI GenBank - and having them pass review - is a labour intensive, iterative process due to the stringent quality requirements that NCBI imposes. These requirements cannot typically be met on the first iteration because they involve checks based on the entirety of NCBI’s presently held data (e.g. contamination checks), checks for the continuously moving target of vendor-specific adaptor sequences, and checks for the validity of gene product names. In many genome annotation projects, these product names are copied over from homologous sequences in related model organisms. This may introduce terminology that is not, or no longer, permitted by NCBI, such as molecular weights and protein structure, organism names, database identifiers, and so on. wgs2ncbi is a standalone Perl package for preparing the results of whole genome sequencing (WGS) and annotation projects to NCBI GenBank. The purpose of the package is to automate responding to NCBI’s reviews by allowing batch corrections to detected problems.
Life, 2018
The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ev... more The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate and test our pipeline's effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: Palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis.
Journal of Open Source Software, 2018
Downloading sequences and sequence information from GenBank and related NCBI databases is often p... more Downloading sequences and sequence information from GenBank and related NCBI databases is often performed via the NCBI API, Entrez. Entrez, however, has a limit on the number of requests, thus downloading large amounts of sequence data in this way can be inefficient. For situations where a large number of Entrez calls is made, downloading may take days, weeks or even months and could result in a user’s IP address being blacklisted from the NCBI services due to server overload. Additionally, Entrez limits the number of entries that can be retrieved at once, requiring a user to develop code for querying in batches. The restez package aims to make sequence retrieval more efficient by allowing a user to download the GenBank database, either in its entirety or in subsets, to their local machine and query this local database instead. This process is more time efficient as GenBank downloads are made via NCBI’s FTP server using compressed sequence files. With a good internet connection and a computer with currently standard capabilities, a database comprising 7 GB of sequence information (i.e. the total sequence data available for Rodentia as of 27 June 2018) can be generated in less than 10 minutes
Systematic Biology, 2016
The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode s... more The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
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Evolutionary biology by Rutger Vos
To analyse the underpinnings of historical drivers of diversity and their contributions to current distributions and future roles in a changing climate, we studied the relationship between ecological niche divergence and phylogenetic signal in tropical carnivorous pitcher plants.
Location
Southeast Asia.
Methods
Estimates of realized ecological niches were reconstructed and plotted along a newly created multilocus molecular phylogeny. Phylogenetic signal was analysed by comparisons of calculated phylogenetic relatedness with ecological niche divergence. Current and projected future potentially suitable habitats were mapped for several species of plants with variable evolutionary histories and distributions.
Results
Highland and lowland species had distinct phylogenetic signals. Higher altitude species had significantly lower molecular divergence as compared with the lowland species, yet ecological niches with less overlap. When projected onto a future climate scenario, highland species lose a greater amount of potentially suitable habitat compared to lower altitude species, and the majority of studied higher altitude species will face an overall loss of future suitable habitat.
Main conclusion
We conclude that distinct phylogenetic signals not only unravel differing evolutionary histories but also show that the implications of species' tolerances to future changing climate vary. Over the past million years, historical climate change shaped the differing evolution and ecological niches of highland and lowland tropical pitcher plant species. Rapid, recent radiations of the higher altitude species are reflected in limited molecular divergence, which is in sharp contrast with the more gradually evolved and genetically distinct lower altitude species in our study. Our projections for future potentially suitable habitats show that on‐going climate shifts will have detrimental effects on especially the higher altitude species due to a narrower niche tolerance and dramatic loss of potentially suitable habitat.
Nutrition and predation have been considered two primary agents of selection important in the evolution of avian life history traits. The relative importance of these natural selective forces in the evolution of avian embryonic developmental period (EDP) remain poorly resolved, perhaps in part because research has tended to focus on a single, high taxonomic-level group of birds: Order Passeriformes. The marine bird families Alcidae (auks) and Spheniscidae (penguins) exhibit marked variation in EDP, as well as behavioural and ecological traits ultimately linked to EDP. Therefore, auks and penguins provide a unique opportunity to assess the natural selective basis of variation in a key life-history trait at a low taxonomic-level. We used phylogenetic comparative methods to investigate the relative importance of behavioural and ecological factors related to nutrition and predation in the evolution of avian EDP.
Results
Three behavioural and ecological variables related to nutrition and predation risk (i.e., clutch size, activity pattern, and nesting habits) were significant predictors of residual variation in auk and penguin EDP based on models predicting EDP from egg mass. Species with larger clutch sizes, diurnal activity patterns, and open nests had significantly shorter EDPs. Further, EDP was found to be longer among birds which forage in distant offshore waters, relative to those that foraged in near shore waters, in line with our predictions, but not significantly so.
Conclusion
Current debate has emphasized predation as the primary agent of selection driving avian life history diversification. Our results suggest that both nutrition and predation have been important selective forces in the evolution of auk and penguin EDP, and highlight the importance of considering these questions at lower taxonomic scales. We suggest that further comparative studies on lower taxonomic-level groups will continue to constructively inform the debate on evolutionary determinants of avian EDP, as well as other life history parameters.
Bioinformatics by Rutger Vos
To analyse the underpinnings of historical drivers of diversity and their contributions to current distributions and future roles in a changing climate, we studied the relationship between ecological niche divergence and phylogenetic signal in tropical carnivorous pitcher plants.
Location
Southeast Asia.
Methods
Estimates of realized ecological niches were reconstructed and plotted along a newly created multilocus molecular phylogeny. Phylogenetic signal was analysed by comparisons of calculated phylogenetic relatedness with ecological niche divergence. Current and projected future potentially suitable habitats were mapped for several species of plants with variable evolutionary histories and distributions.
Results
Highland and lowland species had distinct phylogenetic signals. Higher altitude species had significantly lower molecular divergence as compared with the lowland species, yet ecological niches with less overlap. When projected onto a future climate scenario, highland species lose a greater amount of potentially suitable habitat compared to lower altitude species, and the majority of studied higher altitude species will face an overall loss of future suitable habitat.
Main conclusion
We conclude that distinct phylogenetic signals not only unravel differing evolutionary histories but also show that the implications of species' tolerances to future changing climate vary. Over the past million years, historical climate change shaped the differing evolution and ecological niches of highland and lowland tropical pitcher plant species. Rapid, recent radiations of the higher altitude species are reflected in limited molecular divergence, which is in sharp contrast with the more gradually evolved and genetically distinct lower altitude species in our study. Our projections for future potentially suitable habitats show that on‐going climate shifts will have detrimental effects on especially the higher altitude species due to a narrower niche tolerance and dramatic loss of potentially suitable habitat.
Nutrition and predation have been considered two primary agents of selection important in the evolution of avian life history traits. The relative importance of these natural selective forces in the evolution of avian embryonic developmental period (EDP) remain poorly resolved, perhaps in part because research has tended to focus on a single, high taxonomic-level group of birds: Order Passeriformes. The marine bird families Alcidae (auks) and Spheniscidae (penguins) exhibit marked variation in EDP, as well as behavioural and ecological traits ultimately linked to EDP. Therefore, auks and penguins provide a unique opportunity to assess the natural selective basis of variation in a key life-history trait at a low taxonomic-level. We used phylogenetic comparative methods to investigate the relative importance of behavioural and ecological factors related to nutrition and predation in the evolution of avian EDP.
Results
Three behavioural and ecological variables related to nutrition and predation risk (i.e., clutch size, activity pattern, and nesting habits) were significant predictors of residual variation in auk and penguin EDP based on models predicting EDP from egg mass. Species with larger clutch sizes, diurnal activity patterns, and open nests had significantly shorter EDPs. Further, EDP was found to be longer among birds which forage in distant offshore waters, relative to those that foraged in near shore waters, in line with our predictions, but not significantly so.
Conclusion
Current debate has emphasized predation as the primary agent of selection driving avian life history diversification. Our results suggest that both nutrition and predation have been important selective forces in the evolution of auk and penguin EDP, and highlight the importance of considering these questions at lower taxonomic scales. We suggest that further comparative studies on lower taxonomic-level groups will continue to constructively inform the debate on evolutionary determinants of avian EDP, as well as other life history parameters.
The outsider packages work through docker – a service that, through OS-level virtualization, enables deployment of isolated software "containers" – and a code-sharing service, e.g. GitHub, to allow a user to install and run, in theory, any external, command-line program or package, on any of the major operating systems (Windows, Linux, OSX).