Broad-scale Comparative Studies Research Articles

Problems with using comparative analyses of avian brain size to test hypotheses of cognitive evolution.

There are multiple hypotheses for the evolution of cognition. The most prominent hypotheses are the Social Intelligence Hypothesis (SIH) and the Ecological Intelligence Hypothesis (EIH), which are often pitted against one another. These hypotheses tend to be tested using broad-scale comparative studies of brain size, where brain size is used as a proxy of cognitive ability, and various social and/or ecological variables are included as predictors. Here, we test how robust conclusions drawn from such analyses may be. First, we investigate variation in brain and body size measurements across >1000 bird species. We demonstrate that there is substantial variation in brain and body size estimates across datasets, indicating that conclusions drawn from comparative brain size models are likely to differ depending on the source of the data. Following this, we subset our data to the Corvides infraorder and interrogate how modelling decisions impact results. We show that model results change substantially depending on variable inclusion, source and classification. Indeed, we could have drawn multiple contradictory conclusions about the principal drivers of brain size evolution. These results reflect concerns from a growing number of researchers that conclusions drawn from comparative brain size studies may not be robust. We suggest that to interrogate hypotheses of cognitive evolution, a fruitful way forward is to focus on testing cognitive performance within and between closely related taxa, with an emphasis on understanding the relationship between informational uncertainty and cognitive evolution.

A Test of Altitude‐Related Variation in Aerobic Metabolism of Andean Birds

Endotherms at high altitude face the combined challenges of cold and hypoxia. Cold increases thermoregulatory costs, and hypoxia may limit both thermogenesis and aerobic exercise capacity. Consequently, in comparisons between closely related highland and lowland taxa, we might expect to observe consistent differences in basal metabolism (BMR), maximal metabolism (MMR), and aerobic scope. Previous broad‐scale comparative studies of birds have revealed no association between BMR and native elevation; however, altitude effects may be detectable in fine‐grained comparisons between pairs of ecologically similar, closely related species that are native to different elevations. Moreover, it remains unknown if exercise‐induced MMR and aerobic scope exhibit consistent patterns of altitude variation. To evaluate whether there is an association between altitude and metabolic rates, we tested for altitude‐related variation in aerobic metabolism in 10 Andean passerines representing five pairs of closely related species with contrasting elevational ranges. We used a paired‐lineage design such that the five pairwise comparisons were phylogenetically independent. In our small sample of Andean passerines, we found a significant effect of elevation on mass‐corrected BMR, MMR, and aerobic scope in most but not all cases. BMR and MMR were significantly higher for the high‐elevation species in three pairs, two of which also had a significantly higher aerobic scope at high‐elevation. One pair did not exhibit significant elevational differences in BMR, MMR, or aerobic scope. Overall, we could not document a uniformly consistent elevational trend in the species analyzed.

A test of altitude-related variation in aerobic metabolism of Andean birds.

Endotherms at high altitude face the combined challenges of cold and hypoxia. Cold increases thermoregulatory costs, and hypoxia may limit both thermogenesis and aerobic exercise capacity. Consequently, in comparisons between closely related highland and lowland taxa, we might expect to observe consistent differences in basal metabolic rate (BMR), maximal metabolic rate (MMR) and aerobic scope. Broad-scale comparative studies of birds reveal no association between BMR and native elevation, and altitude effects on MMR have not been investigated. We tested for altitude-related variation in aerobic metabolism in 10 Andean passerines representing five pairs of closely related species with contrasting elevational ranges. Mass-corrected BMR and MMR were significantly higher in most highland species relative to their lowland counterparts, but there was no uniform elevational trend across all pairs of species. Our results suggest that there is no simple explanation regarding the ecological and physiological causes of elevational variation in aerobic metabolism.

A Network for Advancing Dendrochronology, Dendrochemistry and Dendrohydrology in South America

Tree-ring research (TRR) in South America (SA) continues to make important contributions in multiple sub-disciplines, including dendrochemistry and dendrohydrology. This report describes some of the advances in TRR in SA presented in a two-day International Meeting Research entitled “An International Network to Promote Advances in Dendrochronology in South America”, organized by the Laboratory of Dendrochronology and Environmental Studies of the Pontifical Catholic University of Valparaiso in Valparaiso, Chile, on January 21–22, 2019. The objective of the meeting was to communicate recent advances in TRR within a network of laboratories in Argentina, Brazil, Chile, Peru, and Uruguay. Novel methodologies and results in dendrochemistry and wood anatomy were also presented by collaborating researchers from German institutions. This report describes some of the research within the subdisciplines of tree-ring science, including dendrochemistry, anatomy and dendrohydrology, and their application to understanding spatio-temporal variability in heavy metal contamination, climate, hydrology, fire regimes and other critical components of South American forest and woodland ecosystems. The meeting demonstrated expansion and diversification of inquiry and applications of TRR in SA, whereby collaboration across research centers has been critical for the advances made in broad-scale comparative studies as well as multi-proxy approaches and the study of global and hemisphere-scale climate phenomena.

Post-fire resprouting capacity of seasonally dry forest species – Two quantitative indices

Qualitative measures of resprouting capacity often fail to capture inter- and intra-species variation, whereas available quantitative methods can be complex and time-consuming, hindering broad-scale comparative studies. Here, we propose two quantitative indices that can be applied in a standard way in different regions. We sampled 1046 plants of 20 dominant species (6 shrubs, 7 trees and 7 tree/shrubs) from the seasonally dry forests of the arid Chaco, central-western Argentina. Sampling was conducted in burned field sites one growing season after fire. For each sampled plant we measured the diameter of the main burned trunk (MTD) and main resprout (MRD), and the number of burned trunks (TN) and resprouts (RN); we then built estimated composite diameters for trunks and resprouts (ECTD and ECRD) and we calculated two alternative Resprouting Capacity Indices: RCI 1 (ECRD/ECTD); and RCI 2 (MRD/MTD). The indices were validated against a measure of Resprouting Vigour (RV) that included detailed measurement of all trunks and resprouts for a subset of sampled plants. In all cases, variables indicative of fire severity were measured and included in the analyses. The RCIs and RV were highly related, both at the species and growth form levels. Fire severity had no significant effect on these relationships, but growth form affected RCI 2. All species were capable of resprouting, showing considerable inter-species variation for the two proposed RCIs. Species rank differed considerably between RCIs and survival-only estimations. RCI 1 was higher in tree/shrubs (i.e. species regarded as trees or shrubs) and trees than in shrubs. All species showed decreasing resprouting capacity with increasing ECTD. Our results support the use of the proposed RCIs as a robust tool to assess resprouting capacity, providing more details than survival-based assessments. Choosing one or the other implies a trade-off between accuracy and simplicity, and may depend on the scale and objective of the study, and resprouting patterns of studied species. Species, growth form and individual plant size are relevant in explaining post-fire resprouting capacity and survival.

Comparative Study of Four TiO2-Based Photocatalysts to Degrade 2,4-D in a Semi-Passive System

In this study, the relative efficiency of four forms of supported titanium dioxide (TiO2) as a photocatalyst to degrade 2,4-dichlorophenoxyacetic acid (2,4-D) in Killex®, a commercially available herbicide was studied. Coated glass spheres, anodized plate, anodized mesh, and electro-photocatalysis using the anodized mesh were evaluated under an ultraviolet – light-emitting diode (UV-LED) light source at λ = 365 nm in a semi-passive mode. Energy consumption of the system was used to compare the efficiency of the photocatalysts. The results showed both photospheres and mesh consumed approximately 80 J/cm3 energy followed by electro-photocatalysis (112.2 J/cm3), and the anodized plate (114.5 J/cm3). Although electro-photocatalysis showed the fastest degradation rate (K = 5.04 mg L−1 h−1), its energy consumption was at the same level as the anodized plate with a lower degradation rate constant of 3.07 mg L−1 h−1. The results demonstrated that three-dimensional nanotubes of TiO2 surrounding the mesh provide superior degradation compared to one-dimensional arrays on the planar surface of the anodized plate. With limited broad-scale comparative studies between varieties of different TiO2 supports, this study provides a comparative analysis of relative degradation efficiencies between the four photocatalytic configurations.

Spatio-temporal variation in late Middle Palaeolithic Neanderthal behaviour: British bout coupé handaxes as a case study

Recent broad-scale comparative studies of Neanderthal lithic assemblages have contrasted previous views of the Middle Palaeolithic as a period of stasis. Throughout the Middle Palaeolithic, ca. 300,000–35,000 years ago, typo-technological changes can be observed in the Neanderthal behavioural repertoire, including trends that are restricted in time and/or space. Such spatio-temporal diversity seems especially apparent in the late Middle Palaeolithic (MIS 5e–3; ca. 125–35 ka BP) and is widely, though not exclusively, expressed through differing bifacial tool types. An often-quoted example is the restricted distribution of bout coupé or flat-butted cordate handaxes in MIS-3 Britain. This paper provides a broader contextualisation of this bout coupé phenomenon; first, in relation to the general reoccurrence of handaxes in late Middle Palaeolithic Western Europe, including comparisons with the Mousterian of Acheulean Tradition (MTA); and second, as a case study to explore behavioural implications of such spatio-temporal variation. Different explanatory factors for the observed patterns are investigated together with potential links to Neanderthal population dynamics. It is concluded that bout coupés represent a genuinely distinct biface form, which was sometimes maintained through the stages of use, and is most parsimoniously explained by regionalised socio-cultural behaviour, implying specific lines of cultural transmission among late Neanderthal groups.

The complete mitochondrial genome of the Chinese longsnout catfish Leiocassis longirostris (Siluriformes: Bagridae) and a time-calibrated phylogeny of ostariophysan fishes

The complete mitogenome sequence of the Chinese longsnout catfish Leiocassis longirostris was determined using long-polymerase chain reaction (long-PCR) and directly sequenced with primer walking method. The complete mtDNA was 16,534 bp in length and contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop), the gene composition/order of which was identical to that observed in most other vertebrates. Phylogenetic relationship of 15 ostariophysan fishes was reconstructed using Bayesian inference and maximum likelihood methods based on a total of 15,658 nucleotides from all the 13 protein-coding, two rRNA, and 22 tRNA genes, using recently developed models of rate autocorrelation, which resolved the phylogenetic relationship of the major ostariophysan lineages with a high statistical support. The present result was consistent with some previous molecular cladistic work which supported the grouping of (((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), Gonorynchiformes), outgroup). The Chinese longsnout catfish together with the Bagrid catfish (both from the same family Bagridae) had a closer affinity with Amblycipitidae than with other four analyzed catfish families. The relaxed molecular clock method incorporated into the program BEAST vl.5.3 was used to estimate divergence dates among ostariophysan lineages, which revealed that the major ostariophysan lineages diversified in the middle Jurassic (around 164.5 million years ago (Mya)) and the split of Leiocassis/Pseudobagrus occurred in the Oligocene to Miocene (8.9-25.1 Mya). The time-calibrated tree generated in this study would provide a powerful evolutionary tool for broad-scale comparative studies of the catfishes and the ostariophysan fishes.

Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila

BackgroundSpeculation regarding the importance of changes in gene regulation in determining major phylogenetic patterns continues to accrue, despite a lack of broad-scale comparative studies examining how patterns of gene expression vary during development. Comparative transcriptional profiling of adult interspecific hybrids and their parental species has uncovered widespread divergence of the mechanisms controlling gene regulation, revealing incompatibilities that are masked in comparisons between the pure species. However, this has prompted the suggestion that misexpression in adult hybrids results from the downstream cascading effects of a subset of genes improperly regulated in early development.ResultsWe sought to determine how gene expression diverges over development, as well as test the cascade hypothesis, by profiling expression in males of Drosophila melanogaster, D. sechellia, and D. simulans, as well as the D. simulans (♀) × D. sechellia (♂) male F1 hybrids, at four different developmental time points (3rd instar larval, early pupal, late pupal, and newly-emerged adult). Contrary to the cascade model of misexpression, we find that there is considerable stage-specific autonomy of regulatory breakdown in hybrids, with the larval and adult stages showing significantly more hybrid misexpression as compared to the pupal stage. However, comparisons between pure species indicate that genes expressed during earlier stages of development tend to be more conserved in terms of their level of expression than those expressed during later stages, suggesting that while Von Baer's famous law applies at both the level of nucleotide sequence and expression, it may not apply necessarily to the underlying overall regulatory network, which appears to diverge over the course of ontogeny and which can only be ascertained by combining divergent genomes in species hybrids.ConclusionOur results suggest that complex integration of regulatory circuits during morphogenesis may lead to it being more refractory to divergence of underlying gene regulatory mechanisms - more than that suggested by the conservation of gene expression levels between species during earlier stages. This provides support for a 'developmental hourglass' model of divergence of gene expression in Drosophila resulting in a highly conserved pupal stage.

Divergence date estimation and a comprehensive molecular tree of extant cetaceans

Cetaceans are remarkable among mammals for their numerous adaptations to an entirely aquatic existence, yet many aspects of their phylogeny remain unresolved. Here we merged 37 new sequences from the nuclear genes RAG1 and PRM1 with most published molecular data for the group (45 nuclear loci, transposons, mitochondrial genomes), and generated a supermatrix consisting of 42,335 characters. The great majority of these data have never been combined. Model-based analyses of the supermatrix produced a solid, consistent phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete (toothed whale) monophyly, stabilized basal odontocete relationships, and completely resolved branching events within Mysticeti (baleen whales) as well as the problematic speciose clade Delphinidae (oceanic dolphins). Only limited conflicts relative to maximum likelihood results were recorded, and discrepancies found in parsimony trees were very weakly supported. We utilized the Bayesian supermatrix tree to estimate divergence dates among lineages using relaxed-clock methods. Divergence estimates revealed rapid branching of basal odontocete lineages near the Eocene-Oligocene boundary, the antiquity of river dolphin lineages, a Late Miocene radiation of balaenopteroid mysticetes, and a recent rapid radiation of Delphinidae beginning approximately 10 million years ago. Our comprehensive, time-calibrated tree provides a powerful evolutionary tool for broad-scale comparative studies of Cetacea.

Sex and differentiation: population genetic divergence and sexual dimorphism in Mexican goodeid fish

Genetic differentiation arises due to the interaction between natural and sexual selection, migration and genetic drift. A potential role of sexual selection in speciation has received much interest, although comparative studies are inconsistent in finding supporting evidence. A poorly tested prediction is that species subject to a higher intensity of sexual selection should show greater genetic differentiation amongst populations because females from these populations should be more choosy in mate choice. The Goodeinae is a group of endemic Mexican fishes in which female choice has driven some species to be morphologically sexually dimorphic, whereas others are relatively monomorphic. Here, we measured population divergence, using microsatellite loci, within four goodeid species which show contrasting levels of sexual dimorphism. We found higher levels of differentiation between populations of the more dimorphic species, implying less gene flow between populations. We also found evidence of higher levels of genetic differences between the sexes within populations of the dimorphic species, consistent with greater dispersal in males. Adjusted for geographic distance, the mean F(ST) for the dimorphic species is 0.25 compared with 0.16 for the less dimorphic species. We conclude that population differentiation is accelerated in more sexually dimorphic species, and that comparative phylogeography may provide a more powerful approach to detecting processes, such as an influence of sexual selection on differentiation, than broad-scale comparative studies.

Insect gas exchange patterns: a phylogenetic perspective

Most investigations of insect gas exchange patterns and the hypotheses proposed to account for their evolution have been based either on small-scale, manipulative experiments, or comparisons of a few closely related species. Despite their potential utility, no explicit, phylogeny-based, broad-scale comparative studies of the evolution of gas exchange in insects have been undertaken. This may be due partly to the preponderance of information for the endopterygotes, and its scarcity for the apterygotes and exopterygotes. Here we undertake such a broad-scale study. Information on gas exchange patterns for the large majority of insects examined to date (eight orders, 99 species) is compiled, and new information on 19 exemplar species from a further ten orders, not previously represented in the literature (Archaeognatha, Zygentoma, Ephemeroptera, Odonata, Mantodea, Mantophasmatodea, Phasmatodea, Dermaptera, Neuroptera, Trichoptera), is provided. These data are then used in a formal, phylogeny-based parsimony analysis of the evolution of gas exchange patterns at the order level. Cyclic gas exchange is likely to be the ancestral gas exchange pattern at rest (recognizing that active individuals typically show continuous gas exchange), and discontinuous gas exchange probably originated independently a minimum of five times in the Insecta.

CLIMATE CHANGE, HURRICANES AND TROPICAL STORMS, AND RISING SEA LEVEL IN COASTAL WETLANDS

Global climate change is expected to affect temperature and precipitation patterns, oceanic and atmospheric circulation, rate of rising sea level, and the frequency, intensity, timing, and distribution of hurricanes and tropical storms. The magnitude of these projected physical changes and their subsequent impacts on coastal wetlands will vary regionally. Coastal wetlands in the southeastern United States have naturally evolved under a regime of rising sea level and specific patterns of hurricane frequency, intensity, and timing. A review of known ecological effects of tropical storms and hurricanes indicates that storm timing, frequency, and intensity can alter coastal wetland hydrology, geomorphology, biotic structure, energetics, and nutrient cycling. Research conducted to examine the impacts of Hurricane Hugo on colonial waterbirds highlights the importance of long-term studies for identifying complex interactions that may otherwise be dismissed as stochastic processes. Rising sea level and even modest changes in the frequency, intensity, timing, and distribution of tropical storms and hurricanes are expected to have substantial impacts on coastal wetland patterns and processes. Persistence of coastal wetlands will be determined by the interactions of climate and anthropogenic effects, especially how humans respond to rising sea level and how further human encroachment on coastal wetlands affects resource exploitation, pollution, and water use. Long-term changes in the frequency, intensity, timing, and distribution of hurricanes and tropical storms will likely affect biotic functions (e.g., community structure, natural selection, extinction rates, and biodiversity) as well as underlying processes such as nutrient cycling and primary and secondary productivity. Reliable predictions of global-change impacts on coastal wetlands will require better understanding of the linkages among terrestrial, aquatic, wetland, atmospheric, oceanic, and human components. Developing this comprehensive understanding of the ecological ramifications of global change will necessitate close coordination among scientists from multiple disciplines and a balanced mixture of appropriate scientific approaches. For example, insights may be gained through the careful design and implementation of broad-scale comparative studies that incorporate salient patterns and processes, including treatment of anthropogenic influences. Well-designed, broad-scale comparative studies could serve as the scientific framework for developing relevant and focused long-term ecological research, monitoring programs, experiments, and modeling studies. Two conceptual models of broad-scale comparative research for assessing ecological responses to climate change are presented: utilizing space-for-time substitution coupled with long-term studies to assess impacts of rising sea level and disturbance on coastal wetlands, and utilizing the moisture-continuum model for assessing the effects of global change and associated shifts in moisture regimes on wetland ecosystems. Increased understanding of climate change will require concerted scientific efforts aimed at facilitating interdisciplinary research, enhancing data and information management, and developing new funding strategies.