Reconstructing the history of life a genetic approach

Humans have always been curious about the origins of life on earth. Many theories and explanations have been offered over the course of human history. When Darwin and Wallace first presented the theory of evolution by natural selection, it led to a great deal of controversy. However, today there is indisputable evidence for this theory. Evolution, according to Darwin, proceeded through ‘Descent with modification’, which simply denoted the passing of traits from parent to offspring, albeit imperfectly. Offspring, while being largely similar to their parents, may show some differences. Over time, these differences may be selected and result in a divergence strong enough for a new species to be formed. This new species is still related to the older one, since it is derived from it. Just like my cousin and I share a common ancestor in the form of a grandfather, species too share common ancestors with other related species. Going sufficiently far back in time, we can actually trace the ancestor for all life on earth (about 3.8 billion years ago). Therefore, we can reconstruct the history of life on earth by carefully reconstructing relationships between species

Complete assembly of a dengue virus type 3 genome from a recent genotype III clade by metagenomic sequencing of serum.

Background: Mosquito-borne flaviviruses, such as dengue and Japanese encephalitis virus (JEV), cause life-threatening diseases, particularly in the tropics. Methods: Here we performed unbiased metagenomic sequencing of RNA extracted from the serum of four patients and the plasma of one patient, all hospitalized at a tertiary care centre in South India with severe or prolonged febrile illness, together with the serum from one healthy control, in 2014. Results: We identified and assembled a complete dengue virus type 3 sequence from a case of severe dengue fever. We also identified a small number of JEV sequences in the serum of two adults with febrile illness, including one with severe dengue. Phylogenetic analysis revealed that the dengue sequence belonged to genotype III. It has an estimated divergence time of 13.86 years from the most highly related Indian strains. In total, 11 amino acid substitutions were predicted for this strain in the antigenic envelope protein, when compared to the parent strain used for development of the first commercial dengue vaccine.  Conclusions: We demonstrate that both genome assembly and detection of a low number of viral sequences are possible through the unbiased sequencing of clinical material. These methods may help ascertain causal agents for febrile illnesses with no known cause

A primer to infectious disease epidemiology

Infectious diseases, like the ‘novel’ coronavirus pandemic, are amongst the leading causes of death across the world. What are infectious diseases? Where do such diseases come from? How do they spread? How do we study them? And how do human societies combat or limit their spread

An arachnid’s guide to be an ant: morphological and behavioural mimicry in antmimicking spiders

Batesian mimicry imposes several challenges to mimics and evokes adaptations in multiple sensory modalities. Myrmecomorphy, morphological and behavioral resemblance to ants, is seen in over 2000 arthropod species. Ant-like resemblance is observed in at least 13 spider families despite spiders having a distinct body plan compared to ants. Quantifying the extent to which spiders’ shape, size, and behavior resemble model ants will allow us to comprehend the evolutionary pressures that have facilitated myrmecomorphy. Myrmaplata plataleoides are ‘accurate’ mimics of the weaver ants, Oecophylla smaragdina. In this study, we quantify the speed of movement of model, mimic, and non-mimetic jumping spiders. We use traditional and geometric morphometrics to quantify traits such as foreleg and hindleg size, body shape between the model ant, mimic, and non-mimics. Our results suggest that while the mimics closely resemble the model ants in speed of movement, they occupy an intermediate morphological space compared to the model ants and non-mimics. We suggest that ant-mimicking spiders are better at mimicking ants’ locomotory movement than morphology and overall body shape. Our study provides a framework to understand the multimodal nature of mimicry and helps discern the relative contributions of such traits that drive mimetic accuracy in ant-mimicking spiders

Past influences present: Mammalian species from different biogeographic pools sort environmentally in the Indian subcontinent

Diversity-environment relationships are distinct across species pools, and as a result species from different biogeographic pools have different environmental preferences. Regional communities are drawn from available biogeographic pools, subject to environmental and dispersal constraints. Does shared biogeographic history of taxa lead to similar relationships with the environment? We test this idea in the Indian subcontinent, which is at the confluence of multiple biogeographic regions resulting in species from multiple biogeographic pools being distributed here. Species were classified as belonging to four biogeographic affinities based on their geographic distributions: eastern, northern, western and endemic. We investigated spatial patterns of species richness for all mammals (over 1° x 1° grid cells), for each biogeographic group and for 5 major mammalian orders. Generalized Additive Models (GAM) were used to investigate environment-diversity relationship for all mammals, each biogeographic group, and for major mammalian orders in the Indian subcontinent. Species richness of all mammals was found to be highest in the montane regions of the Eastern Himalayas and the Western Ghats. Species richness of each biogeographic group was highest at the border it shared with Asia, in the direction of immigration from Asia. Environment and spatial variables were both correlated with species richness in the Indian subcontinent and each biogeographic group showed a distinct richness-environment relationship. Additionally, biogeographic groups sorted along environmental space, in keeping with our predictions based on their global distributions. Finally, analyses across mammalian orders had low predictive value, suggesting that shared phylogenetic history is relatively less important than biogeographic ancestry in determining relationships to environment. We conclude that historical factors such as immigration and the distinct evolutionary histories of species impact species richness patterns in the Indian subcontinent. Our results provide insights into drivers of regional community assembly in transition zones where multiple biogeographic species pools co-exist

An arachnid’s guide to being an ant: morphological and behavioral mimicry in ant-mimicking spiders

Batesian mimicry imposes several challenges to mimics and evokes adaptations in multiple sensory modalities. Myrmecomorphy, morphological and behavioral resemblance to ants, is seen in over 2000 arthropod species. Ant-like resemblance is observed in at least 13 spider families despite spiders having a distinct body plan compared to ants. Quantifying the extent to which spiders’ shape, size, and behavior resemble model ants will allow us to comprehend the evolutionary pressures that have facilitated myrmecomorphy. Myrmaplata plataleoides are thought to closely resemble weaver ants, Oecophylla smaragdina. In this study, we quantify the speed of movement of model, mimic, and non-mimetic jumping spiders. We use traditional and geometric morphometrics to quantify traits such as foreleg size and hindleg size, body shape between the model ant, mimic, and non-mimics. Our results suggest that while the mimics closely resemble the model ants in speed of movement, they occupy an intermediate morphological space compared to the model ants and non-mimics. Ant-mimicking spiders are better at mimicking ants’ locomotory movement than morphology and overall body shape. Some traits may compensate others, suggesting differential selection on these mimetic traits. Our study provides a framework to understand the multimodal nature of mimicry and helps discern the relative contributions of such traits that drive mimetic accuracy in ant-mimicking spiders

Past influences present: Mammalian species from different biogeographic pools sort environmentally in the Indian subcontinent

Diversity-environment relationships are distinct across species pools, and as a result species from different biogeographic pools have different environmental preferences. Regional communities are drawn from available biogeographic pools, subject to environmental and dispersal constraints. Does shared biogeographic history of taxa lead to similar relationships with the environment? We test this idea in the Indian subcontinent, which is at the confluence of multiple biogeographic regions resulting in species from multiple biogeographic pools being distributed here. Species were classified as belonging to four biogeographic affinities based on their geographic distributions: eastern, northern, western and endemic. We investigated spatial patterns of species richness for all mammals (over 1° x 1° grid cells), for each biogeographic group and for 5 major mammalian orders. Generalized Additive Models (GAM) were used to investigate environment-diversity relationship for all mammals, each biogeographic group, and for major mammalian orders in the Indian subcontinent. Species richness of all mammals was found to be highest in the montane regions of the Eastern Himalayas and the Western Ghats. Species richness of each biogeographic group was highest at the border it shared with Asia, in the direction of immigration from Asia. Environment and spatial variables were both correlated with species richness in the Indian subcontinent and each biogeographic group showed a distinct richness-environment relationship. Additionally, biogeographic groups sorted along environmental space, in keeping with our predictions based on their global distributions. Finally, analyses across mammalian orders had low predictive value, suggesting that shared phylogenetic history is relatively less important than biogeographic ancestry in determining relationships to environment. We conclude that historical factors such as immigration and the distinct evolutionary histories of species impact species richness patterns in the Indian subcontinent. Our results provide insights into drivers of regional community assembly in transition zones where multiple biogeographic species pools co-exist

Inferring critical thresholds of ecosystem transitions from spatial data

Ecosystems can undergo abrupt transitions between alternative stable states when the driver crosses a critical threshold. Dynamical systems theory shows that when ecosystems approach the point of loss of stability associated with these transitions, they take a long time to recover from perturbations, a phenomenon known as critical slowing down. This generic feature of dynamical systems can offer early warning signals of abrupt transitions. However, these signals are qualitative and cannot quantify the thresholds of drivers at which transition may occur. Here, we propose a method to estimate critical thresholds from spatial data. We show that two spatial metrics, spatial variance and autocorrelation of ecosystem state variable, computed along driver gradients can be used to estimate critical thresholds. First, we investigate cellular-automaton models of ecosystem dynamics that show a transition from a high-density state to a bare state. Our models show that critical thresholds can be estimated as the ecosystem state and the driver values at which spatial variance and spatial autocorrelation of the ecosystem state are maximum. Next, to demonstrate the application of the method, we choose remotely sensed vegetation data (Enhanced Vegetation Index, EVI) from regions in central Africa and northeast Australia that exhibit alternative states in woody cover. We draw transects (8 x 90 km) that span alternative stable states along rainfall gradients. Our analyses of spatial variance and autocorrelation of EVI along transects yield estimates of critical thresholds. These estimates match reasonably well with those obtained by an independent method that uses large-scale (250 x 200 km) spatial data sets. Given the generality of the principles that underlie our method, our method can be applied to a variety of ecosystems that exhibit alternative stable states

Data from: Climatic and geographic barriers drive distributional patterns of bird phenotypes within peninsular India

Modern phylogenetic data provide unparalleled ability to test biogeographic paradigms, often suggested by differences in species distribution patterns. However, such approaches have been applied less at regional scales, particularly in Asia. In the absence of such data, we examine if concordance of distributional patterns for phenotypes (subspecies) suggest potential biogeographic barriers for birds in peninsular India. Specifically, we examine climatic and physical factors that might limit phenotype distributions in this region. Various physical, vegetation and climatic barriers were demarcated to identify potential biogeographic units within peninsular India. We then collated occurrence of endemic or disjunctly distributed species and subspecies within these units using published range maps. We also quantified turnover between potential units, allowing us to identify significant biogeographic barriers. Three time-step climate data (Last Glacial Maxima, mid-Holocene and present) enabled us to examine differences between these potential biogeographic regions through time. The Palk Straits, followed by the Goa Gap (∼ 16°N) and the Godavari River emerged as the major barriers in this region. The Palk Straits and Godavari are physical barriers while Goa Gap appears to be a climate-mediated ecological divide. Mountain barriers like the Palghat Gap are not the most significant barriers as previously thought. Climatically intermediate regions appeared unstable in the past and showed inconsistent affinities to different geographic units across families. We suggest that relative climatic stability of the wet regions of the southern western Ghats could be responsible for high subspecies endemism here. Our approach provides hypotheses that can be tested with comparative multi-species phylogeographic data in the future