Estimating Pan evolutionary history from nucleotide site patterns

Introgression appears increasingly ubiquitous in the evolutionary history of various taxa, including humans. However, accurately estimating introgression is difficult, particularly when 1) there are many parameters, 2) multiple models fit the data well, and 3) parameters are not simultaneously estimated. Here, we use the software Legofit to investigate the evolutionary history of bonobos (Pan paniscus) and chimpanzees (P. troglodytes) using whole genome sequences. This approach 1) ignores within-population variation, reducing the number of parameters requiring estimation, 2) allows for model selection, and 3) simultaneously estimates all parameters. We tabulated site patterns from the autosomes of 71 bonobos and chimpanzees representing all five extant Pan lineages. We then compared previously proposed demographic models and estimated parameters using a deterministic approach. We further considered sex bias in Pan evolutionary history by analyzing the site patterns from the X chromosome. Introgression from bonobos into the ancestor of eastern and central chimpanzees and from western into eastern chimpanzees best explained the autosomal site patterns. This second event was substantial with an estimated 0.21 admixture proportion. Estimates of effective population size and most divergence dates are consistent with previous findings; however, we observe a deeper divergence within chimpanzees at 987 ka. Finally, we identify male-biased reproduction in Pan evolutionary history and suggest that western to eastern chimpanzee introgression was driven by western males mating with eastern females.

Plagued by a cryptic clock: Insight and issues from the global phylogeny of Yersinia pestis

Plague has an enigmatic history as a zoonotic pathogen. This potentially devastating infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. We perform a detailed Bayesian evaluation of temporal signal in subsets of these data and demonstrate that a Y. pestis-wide molecular clock model is unstable. To resolve this, we devised a new approach in which each Y. pestis population was assessed independently. This enabled us to recover significant temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics. Finally, we identify key historical data sets that can be used in future research, which will complement the strengths and mitigate the weaknesses of genomic data.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

With over 380,000 described species and possibly several million more yet unnamed, beetles represent the most biodiverse animal order. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here we use a dataset of 68 single-copy nuclear protein coding genes sampling 129 out of the 194 recognized extant families as well as the first comprehensive set of fully-justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov., and Staphyliniformia sensu nov., alongside changes below the superfamily level. The heterogeneous former superfamily Cucujoidea is divided into three monophyletic groups: Erotyloidea stat. nov., Nitiduloidea stat. nov., and Cucujoidea sensu nov. Our divergence time analysis recovered an evolutionary timescale congruent with the fossil record: a late Carboniferous origin of Coleoptera, a late Paleozoic origin of all modern beetle suborders, and a Triassic–Jurassic origin of most extant families. While fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution, many polyphagan superfamilies exhibited increases in richness with Cretaceous flowering plants.

A Bayesian approach to the classification of Tungusic languages

The Tungusic language family is comprised of languages spoken in Siberia, the Russian Far East, Northeast China and Xinjiang. There is a general consensus that these languages are genealogically related and descend from a common ancestral language. Nevertheless, there is considerable disagreement with regard to the internal structure of the Tungusic family and the time depth of its separation into daughter languages. Here we use computational Bayesian phylogenetic methods to generate a phylogeny of Tungusic languages and estimate the time-depth of the family. Our analysis is based on the recently introduced Leipzig-Jakarta-Jena list, a dataset of 254 basic vocabulary items collected for 21 Tungusic doculects. Our results are consistent with two basic classifications previously proposed in the literature, notably a Manchu-Tungusic classification, in which the break-up of Jurchenic constitutes the first split in the tree, as well as a North-South classification, which includes a Jurchenic-Nanaic and an Orochic-Ewenic branch. In addition, we obtain a time-depth for the age of Proto-Tungusic between the 8th century BC and the 12th century AD (95% highest posterior density interval). Previous classifications of Tungusic were based on both classical historical comparative linguistic and lexicostatistic approaches, but the application of Bayesian phylogenetic methods to the Tungusic languages has not so far been attempted. In contrast to previous approaches, our Bayesian analysis adds an understanding of the statistical robustness of the proposed branches and infers absolute divergence dates, allowing variation of rates of change across branches and cognate sets. In this way, our research provides a reliable quantitative basis for previous estimates based on classical historical linguistic and lexicostatistic approaches.

Patterns of coevolution between ambrosia beetle mycangia and the Ceratocystidaceae, with five new fungal genera and seven new species

Ambrosia beetles farm specialised fungi in sapwood tunnels and use pocket-like organs called mycangia to carry propagules of the fungal cultivars. Ambrosia fungi selectively grow in mycangia, which is central to the symbiosis, but the history of coevolution between fungal cultivars and mycangia is poorly understood. The fungal family Ceratocystidaceae previously included three ambrosial genera (Ambrosiella, Meredithiella, and Phialophoropsis), each farmed by one of three distantly related tribes of ambrosia beetles with unique and relatively large mycangium types. Studies on the phylogenetic relationships and evolutionary histories of these three genera were expanded with the previously unstudied ambrosia fungi associated with a fourth mycangium type, that of the tribe Scolytoplatypodini. Using ITS rDNA barcoding and a concatenated dataset of six loci (28S rDNA, 18S rDNA, tef1-α, tub, mcm7, and rpl1), a comprehensive phylogeny of the family Ceratocystidaceae was developed, including Inodoromyces interjectus gen. & sp. nov., a non-ambrosial species that is closely related to the family. Three minor morphological variants of the pronotal disk mycangium of the Scolytoplatypodini were associated with ambrosia fungi in three respective clades of Ceratocystidaceae: Wolfgangiella gen. nov., Toshionella gen. nov., and Ambrosiella remansi sp. nov. Closely-related species that are not symbionts of ambrosia beetles are accommodated by Catunica adiposa gen. & comb. nov. and Solaloca norvegica gen. & comb. nov. The divergent morphology of the ambrosial genera and their phylogenetic placement among non-ambrosial genera suggest three domestication events in the Ceratocystidaceae. Estimated divergence dates for the ambrosia fungi and mycangia suggest that Scolytoplatypodini mycangia may have been the first to acquire Ceratocystidaceae symbionts and other ambrosial fungal genera emerged shortly after the evolution of new mycangium types. There is no evidence of reversion to a non-ambrosial lifestyle in the mycangial symbionts.

120 Years of Untangling the Divaricate Habit: A Review

The evolution of divaricate plants in New Zealand has been the subject of long-running debate among botanists and ecologists. Hypotheses about this remarkable case of convergent evolution have focused mainly on two different types of selective pressures: the Plio-Pleistocene advent of cool, dry climates, or browsing by now-extinct moa. Here, we review the scientific literature relating to the New Zealand divaricates, and present a list of 81 taxa whose architectures fall on the divaricate habit spectrum. We recommend a series of standardised terms to facilitate clear communication about these species. We identify potentially informative areas of research yet to be explored, such as the genetics underlying the establishment and control of this habit. We also review work about similar plants overseas, proposing a list of 47 such species as a first step towards more comprehensive inventories; these may motivate further studies of the ecology, morphology and evolutionary history of these overseas plants which could help shed light on the evolution of their New Zealand counterparts. Finally, we compile published divergence dates between divaricate species and their non-divaricate relatives, which suggest that the divaricate habit is fairly recent (< 10 My) in most cases.

A new species of Lepidodactylus (Squamata: Gekkonidae) from the mountains of northeastern Papua New Guinea: older than the hills

We describe a new species of Lepidodactylus with an unusual distribution across scattered localities in three isolated mountain ranges of northeastern New Guinea. It is a member of the Lepidodactylus pumilus group and can be distinguished from all other Melanesian Lepidodactylus by aspects of size, scalation, digital webbing, and coloration. Previously published genetic and morphological data indicate that the new species is most similar to Lepidodactylus magnus, but it diverged from this species and other close relatives in the mid-Miocene or earlier, potentially on islands of the former South Caroline Arc. Estimated divergence dates between the new species and its sister taxon suggest that cladogenesis occurred before the uplift of the mountains that they currently inhabit. Recent systematic work also emphasizes an apparent pattern of increasing body size with elevation in species from the Lepidodactylus pumilus group from northeastern New Guinea, with the largest species occurring in montane habitats where few or no other gecko species are known. Both lines of evidence are consistent with an existing hypothesis that the Lepidodactylus pumilus group is an old insular lineage within which contemporary species diversity and distributions have been strongly shaped by low ability to effectively compete against other aggressive geckos in species-rich lowland rainforests. The role that biotic interactions may have played in shaping tropical gecko communities along elevational gradients warrants further investigation.

Bayesian phylolinguistics infers the internal structure and the time-depth of the Turkic language family

Despite more than 200 years of research, the internal structure of the Turkic language family remains subject to debate. Classifications of Turkic so far are based on both classical historical–comparative linguistic and distance-based quantitative approaches. Although these studies yield an internal structure of the Turkic family, they cannot give us an understanding of the statistical robustness of the proposed branches, nor are they capable of reliably inferring absolute divergence dates, without assuming constant rates of change. Here we use computational Bayesian phylogenetic methods to build a phylogeny of the Turkic languages, express the reliability of the proposed branches in terms of probability, and estimate the time-depth of the family within credibility intervals. To this end, we collect a new dataset of 254 basic vocabulary items for thirty-two Turkic language varieties based on the recently introduced Leipzig–Jakarta list. Our application of Bayesian phylogenetic inference on lexical data of the Turkic languages is unprecedented. The resulting phylogenetic tree supports a binary structure for Turkic and replicates most of the conventional sub-branches in the Common Turkic branch. We calculate the robustness of the inferences for subgroups and individual languages whose position in the tree seems to be debatable. We infer the time-depth of the Turkic family at around 2100 years before present, thus providing a reliable quantitative basis for previous estimates based on classical historical linguistics and lexicostatistics.

Molecular Analysis of the Complete Genome of a Simian Foamy Virus Infecting Hylobates pileatus (pileated gibbon) Reveals Ancient Co-Evolution with Lesser Apes

Foamy viruses (FVs) are complex retroviruses present in many mammals, including nonhuman primates, where they are called simian foamy viruses (SFVs). SFVs can zoonotically infect humans, but very few complete SFV genomes are available, hampering the design of diagnostic assays. Gibbons are lesser apes widespread across Southeast Asia that can be infected with SFV, but only two partial SFV sequences are currently available. We used a metagenomics approach with next-generation sequencing of nucleic acid extracted from the cell culture of a blood specimen from a lesser ape, the pileated gibbon (Hylobates pileatus), to obtain the complete SFVhpi_SAM106 genome. We used Bayesian analysis to co-infer phylogenetic relationships and divergence dates. SFVhpi_SAM106 is ancestral to other ape SFVs with a divergence date of ~20.6 million years ago, reflecting ancient co-evolution of the host and SFVhpi_SAM106. Analysis of the complete SFVhpi_SAM106 genome shows that it has the same genetic architecture as other SFVs but has the longest recorded genome (13,885-nt) due to a longer long terminal repeat region (2,071 bp). The complete sequence of the SFVhpi_SAM106 genome fills an important knowledge gap in SFV genetics and will facilitate future studies of FV infection, transmission, and evolutionary history.

Genetic data of museum specimens allow for inferring evolutionary history of the cosmopolitan genusSirthenea(Heteroptera: Reduviidae)

Among the 30 known genera within subfamily Peiratinae, only the genusSirtheneahas a cosmopolitan distribution. The results of our studies are the first comprehensive analysis concerning one of the representatives of mentioned subfamily based on joint phylogenetic analyses of molecular and morphological data as well as molecular dating. A total of 32 species were included into the dataset with all known species of the genusSirthenea. Material of over 400 dry specimens was examined for the morphological part of this study. The cosmopolitan distribution ofSirtheneaand the inaccessibility of specimens preserved in alcohol required the extraction of DNA from the dried skeletal muscles of specimens deposited in 24 entomological collections. The oldest specimens used for the successful extraction and sequencing were collected more than 120 years ago in India. We performed Bayesian Inference analyses of molecular and morphological data separately, as well as combined analysis. The molecular and morphological data obtained during our research verify the correlation of the divergence dates of all knownSirtheneaspecies. Results of the relaxed molecular clock analysis of the molecular data show that, the genusSirtheneastarted diverging in the Late Cretaceous into two clades, which subsequently began to branch off in the Paleocene. Our results of phylogenetic analyses suggest that thefossula spongiosaand its development could be one of the most important morphological characters in the evolution of the genus, most likely associated with the ecological niche inhabited bySirthenearepresentatives. Confirmation of the results obtained in our studies is the reconciliation of the evolutionary history ofSirtheneawith the biogeographical processes that have shaped current global distribution of the genus.