The effect of mainland dynamics on data and parameter estimates in island biogeography

Understanding macroevolution on islands requires knowledge of the closest relatives of island species on the mainland. The evolutionary relationships between island and mainland species can be reconstructed using phylogenies, to which models can be fitted to understand the dynamical processes of colonisation and diversification. But how much information on the mainland is needed to gain insight into macroevolution on islands? Here we first test whether species turnover on the mainland and incomplete mainland sampling leave recognisable signatures in community phylogenetic data. We find predictable phylogenetic patterns: colonisation times become older and the perceived proportion of endemic species increases as mainland turnover and incomplete knowledge increase. We then analyse the influence of these factors on the inference performance of the island biogeography model DAISIE, a whole-island community phylogenetic model that assumes that mainland species do not diversify, and that the mainland is fully sampled in the phylogeny. We find that colonisation and diversification rate are estimated with little bias in the presence of mainland extinction and incomplete sampling. By contrast, the rate of anagenesis is overestimated under high levels of mainland extinction and incomplete sampling, because these increase the perceived level of island endemism. We conclude that community-wide phylogenetic and endemism datasets of island species carry a signature of mainland extinction and sampling. The robustness of parameter estimates suggests that island diversification and colonisation can be studied even with limited knowledge of mainland dynamics.

Tube-dwelling in early animals exemplified by Cambrian scalidophoran worms

Background The radiation of ecdysozoans (moulting animals) during the Cambrian gave rise to panarthropods and various groups of worms including scalidophorans, which played an important role in the elaboration of early marine ecosystems. Although most scalidophorans were infaunal burrowers travelling through soft sediment at the bottom of the sea, Selkirkia lived inside a tube. Results We explore the palaeobiology of these tubicolous worms, and more generally the origin and evolutionary significance of tube-dwelling in early animals, based on exceptionally preserved fossils from the early Cambrian Chengjiang Lagerstätte (Stage 3, China) including a new species, Selkirkia transita sp. nov. We find that the best phylogenetic model resolves Selkirkia as a stem-group priapulid. Selkirkia secreted a protective cuticular thickening, the tube, inside which it was able to move during at least part of its life. Partly based on measured growth patterns, we construe that this tube was separated from the trunk during a moulting process that has no direct equivalent in other scalidophorans. Although the ontogeny of Selkirkia is currently unknown, we hypothesize that its conical tube might have had the same ecological function and possibly even deep development origin as the lorica, a protective cuticular thickening found in larval priapulids and adult loriciferans. Selkirkia is seen as a semi-sedentary animal capable of very shallow incursions below the water/sediment interface, possibly for feeding or during the tube-secreting phase. Brachiopod epibionts previously reported from the Xiaoshiba Lagerstätte (ca. 514 Ma) also presumably occur in Selkirkia sinica from Chengjiang (ca. 518 Ma). Conclusions Our critical and model-based approach provides a new phylogenetic framework for Scalidophora, upon which to improve in order to study the evolution of morphological characters in this group. Tube-dwelling is likely to have offered Selkirkia better protection and anchoring to sediment and has developed simultaneously in other Cambrian animals such as hemichordates, annelids or panarthropods. Often lost in modern representatives in favour of active infaunal lifestyles, tube-dwelling can be regarded as an early evolutionary response of various metazoans to increasing environmental and biological pressure in Cambrian marine ecosystems.

Diversification Declines in Major Dinosaurian Clades are not Because of Edge Effects or Incomplete Fossil Sampling

Signatures of catastrophic mass extinctions have long been reported to be obscured by the edge effect where taxonomic diversity appears to decline gradually. Similarly, models of diversification based on splitting of branches on a phylogenetic tree might also be affected by undersampling of divergences towards the edge. The implication is that long-term declines in diversification recovered from such models – e.g., in dinosaurs – may be artefacts of unsampled divergences. However, this effect has never been explicitly tested in a phylogenetic model framework – i.e., whether phylogenetic nodes (speciation events) close to the edge are under-sampled and if diversification declines are artefacts of such under-sampling. Here, we test whether dinosaur species in temporal proximity to the Cretaceous-Paleogene mass extinction event are associated with fewer nodes than expected, and whether this under-sampling can account for the diversification decline. We find on the contrary that edge taxa have higher numbers of nodes than expected and that accounting for this offset does not affect the diversification decline. We demonstrate that the observed diversification declines in the three major dinosaurian clades in the Late Cretaceous are not artefacts of the edge effect.

Evolution of initiation rites during the Austronesian dispersal

As adaptive systems, kinship and its accompanying rules have co-evolved with elements of complex societies, including wealth inheritance, subsistence, and power relations. Here we consider an aspect of kinship evolution in the Austronesian dispersal that began from about 5500 BP in Taiwan, reaching Melanesia about 3200 BP, and dispersing into Micronesia by 1500 BP. Previous, foundational work has used phylogenetic comparative methods and ethnolinguistic information to infer matrilocal residence in proto-Austronesian societies. Here we apply Bayesian phylogenetic analyses to a data set on Austronesian societies that combines existing data on marital residence systems with a new set of ethnographic data, introduced here, on initiation rites. Transition likelihoods between cultural-trait combinations were modeled on an ensemble of 1000 possible Austronesian language trees, using Reversible Jump Markov Chain Monte Carlo (RJ-MCMC) simulations. Compared against a baseline phylogenetic model of independent evolution, a phylogenetic model of correlated evolution between female and male initiation rites is substantially more likely (log Bayes factor: 17.9). This indicates, over the generations of Austronesian dispersal, initiation rites were culturally stable when both female and male rites were in the same state (both present or both absent), yet relatively unstable for female-only rites. The results indicate correlated phylogeographic evolution of cultural initiation rites in the prehistoric dispersal of Austronesian societies across the Pacific. Once acquired, male initiation rites were more resilient than female-only rites among Austronesian societies.

Evolution of butterfly-plant networks over time, as revealed by Bayesian inference of host repertoire

The study of herbivorous insects underpins much of the theory that concerns the evolution of species interactions. In particular, Pieridae butterflies and their host plants have served as a model system for studying evolutionary arms-races. To learn more about how the two lineages co-evolved over time, we reconstructed ecological networks and network properties using a phylogenetic model of host-repertoire evolution. In tempo and mode, host-repertoire evolution in Pieridae is slower and more conservative when compared to similar model-based estimates previously obtained for another butterfly clade, Nymphalini. Our study provides detailed insights into how host shifts, host range expansions, and recolonizations of ancestral hosts have shaped the Pieridae-angiosperm network through a phase transition from a disconnected to a connected network. Our results demonstrate the power of combining network analysis with Bayesian inference of host repertoire evolution in understanding how complex species interactions change over time.

Numeral classifiers and number marking in Indo-Iranian

This paper investigates the origins of sortal numeral classifiers in the Indo-Iranian languages. While these are often assumed to result from contact with non-Indo-European languages, an alternative possibility is that classifiers developed as a response to the rise of optional plural marking. This alternative is in line with the so-called Greenberg-Sanches-Slobin (henceforth GSS) generalization. The GSS generalization holds that the presence of sortal numeral classifiers across languages is negatively correlated with obligatory plural marking on nouns. We assess the extent to which Indo-Iranian classifier development is influenced by loosening of restrictions on plural marking using a sample of 65 languages and a Bayesian phylogenetic model, inferring posterior distributions over evolutionary transition rates between typological states and using these rates to reconstruct the history of classifiers and number marking throughout Indo-Iranian, constrained by historically attested states. We find broad support for a diachronically oriented construal of the GSS generalization, but find no evidence for a strong bias against the synchronic co-occurrence of classifiers and obligatory plural marking. Inspection of the most likely diachronic trajectories in individual lineages in the tree shows a stronger effect of the GSS among Iranian languages than Indo-Aryan languages. Taken as a whole, these findings suggest that the association of classifiers and optional number marking in Indo-Iranian is neither solely the effect of universal mechanisms nor of the contingency of local contact histories.

Computational Analysis of Distance based Phylogenetic Tree for Azotobacter Species

Phylogenetic tree is a pictorial representation of evolutionary relationships between organisms. It is important method to analyze the biological data. Phylogenetic trees are based on two methods : Distance based and Character based. Phylogenetic tree are used comparative analysis of any organism like human Beings, Animals, Bacteria, Viruses and Fungi’s etc. In this paper we compare 12 different nucleotide sequences of Azotobacter species having linear DNA of 999 BP as maximum size using substitution model and phylogenetic model. In this study two different models name P-Distance and Jukes cantor model are used and helped in finding UPGMA or Neighbour joining method efficiency in evaluating the similarity and dissimilarity of bacterial species. This paper gives influence in reconciliation of Azotobacter species to produce phylogram with informative branch lengths. This further leads to analyze and understand various expressive characters of Azotobacter in agriculture field.

Bayesian inference of ancestral host-parasite interactions under a phylogenetic model of host repertoire evolution

Intimate ecological interactions, such as those between parasites and their hosts, may persist over long time spans, coupling the evolutionary histories of the lineages involved. Most methods that reconstruct the coevolutionary history of such associations make the simplifying assumption that parasites have a single host. Many methods also focus on congruence between host and parasite phylogenies, using cospeciation as the null model. However, there is an increasing body of evidence suggesting that the host ranges of parasites are more complex: that host ranges often include more than one host and evolve via gains and losses of hosts rather than through cospeciation alone. Here, we develop a Bayesian approach for inferring coevolutionary history based on a model accommodating these complexities. Specifically, a parasite is assumed to have a host repertoire, which includes both potential hosts and one or more actual hosts. Over time, potential hosts can be added or lost, and potential hosts can develop into actual hosts or vice versa. Thus, host colonization is modeled as a two-step process, which may potentially be influenced by host relatedness or host traits. We first explore the statistical behavior of our model by simulating evolution of host-parasite interactions under a range of parameters. We then use our approach, implemented in the program RevBayes, to infer the coevolutionary history between 34 Nymphalini butterfly species and 25 angiosperm families.