A simple island biodiversity model is robust to trait dependence in diversification and colonization rates

The application of state-dependent speciation and extinction (SSE) models to phylogenetic trees has revealed an important role for traits in diversification. However, this role remains comparatively unexplored on islands, which can include multiple independent clades resulting from different colonization events. Here, we perform a robustness study to identify how trait-dependence in rates of island colonization, extinction and speciation (CES rates) affects the estimation accuracy of a phylogenetic model that assumes no rate variation between trait states. We extend the DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) simulation model to include state-dependent rates, and evaluate the robustness of the DAISIE inference model using simulated data. Our results show that when the CES rate differences between trait states are moderate, DAISIE shows negligible error for a variety of island diversity metrics. However, for large differences in speciation rates, we find large errors when reconstructing clade size variation and non-endemic species diversity through time. We conclude that for many biologically realistic scenarios with trait-dependent speciation and colonization, island diversity dynamics can be accurately estimated without the need to explicitly model trait dynamics. Nonetheless, our new simulation model may provide a useful tool for studying patterns of trait variation.

Edaphic invertebrate diversity around the reservoir of a small hydroelectric power station in southern Brazil

To meet the growing demand for electricity, considerable effort has been invested in the construction of hydroelectric stations in Brazil. The environmental impacts caused by these projects have been significant, especially on fauna. To evaluate the biodiversity of edaphic invertebrates, a study was performed in an area surrounding a small hydroelectric station of Flor do Sertão, in the Santa Catarina state, Brazil, covering three distances (5, 15 and 30 meters) from the flooded region of the reservoir. From December 2010 to June 2011, surveys of edaphic invertebrates were performed by pitfall traps. The invertebrates collected at each distance were compared and their diversity was calculated through Hill numbers. The dynamics were analyzed through the Shannon index exponential and the inverse Simpson index, and correlated climatic variables to invertebrate diversity. A total of 14,074 specimens were collected from 24 taxonomic groups (Order). The analyses according to size and sample coverage showed few differences in invertebrate diversity between the distances. Values of richness and diversity of common groups are similar for all distances. There is a trend decrease in diversity dynamics for common individuals, with a strong decline in June. The diversity of edaphic invertebrates exhibited high correlation with temperature and no correlation with pluviosity.

Spatial approach to analyzing dynamics of racial diversity in large U.S. cities: 1990–2000–2010

Over the last several decades large U.S. cities became increasingly racially diverse. Understanding spatio-temporal dynamics of this significant social change and identifying its broad trends is important for numerous stakeholders. High resolution population grids, which recently become available for the entire conterminous U.S. and for three-time points from 1990 to 2010, are an ideal dataset for analyzing dynamics of racial diversity. Their value to diversity analysis has been already demonstrated at the level of the entire U.S. as well as at the level of an individual city.In this paper, we demonstrate their value for performing a survey aimed at synthesizing diversity dynamics from different cities in order to identify prevalent nationwide trends. Our survey consists of 41 large cities. 1990-2000-2010 snapshots of racial conditions at each city are provided by respective grids in which each cell is assigned one of nine possible diversity/dominant race categories. All cells with the same diversity label constitute a zone which we refer to as community and measure using a percentage of landscape (PLAND) and an aggregation index (AI) metrics. The inclusion of the AI metric makes it possible to determine not only whether a given community grows or shrinks but also whether it’s merging or fragmenting. We analyze spatio-temporal evolution of communities by tracking changes in the pairs of the values of these metrics. To simplify we categorize these changes into eight categories resulting in 64 possible change trajectories for each community. Trajectories are histogrammed to reveal the variety of scarcity of possible modes of change. Frequent trajectories are identified with broad trends. Eight such trends are identified, they represent the most prevalent racial dynamics in the U.S. during the decades of 1990-2010. Two trends correspond to the decay of whites-only and blacks-only communities. The remaining six trends correspond to the expansion of Hispanics, Asian, and racially diverse communities. Trends do not show regional dependence, they truly reflect profound social change occurring across the entire U.S.

Influence of historical changes in tropical reef habitat on the diversification of coral reef fishes

Past environmental changes are expected to have profoundly impacted diversity dynamics through time. While some previous studies showed an association between past climate changes or tectonic events and important shifts in lineage diversification, it is only recently that past environmental changes have been explicitly integrated in diversification models to test their influence on diversification rates. Here, we used a global reconstruction of tropical reef habitat dynamics during the Cenozoic and phylogenetic diversification models to test the influence of (i) major geological events, (ii) reef habitat fragmentation and (iii) reef area on the diversification of 9 major clades of tropical reef fish (Acanthuridae, Balistoidea, Carangoidea, Chaetodontidae, Haemulinae, Holocentridae, Labridae, Pomacentridae and Sparidae). The diversification models revealed a weak association between paleo-habitat changes and diversification dynamics. Specifically, the fragmentation of tropical reef habitats over the Cenozoic was found to be a driver of tropical reef fish diversification for 2 clades. However, overall, our approach did not allow the identification of striking associations between diversification dynamics and paleo-habitat fragmentation in contrast with theoretical model’s predictions.

Predatory Bacteria Select for Sustained Prey Diversity

Predator impacts on prey diversity are often studied among higher organisms over short periods, but microbial predator-prey systems allow examination of prey-diversity dynamics over evolutionary timescales. We previously showed that Escherichia coli commonly evolved minority mucoid phenotypes in response to predation by the bacterial predator Myxococcus xanthus by one time point of a coevolution experiment now named MyxoEE-6. Here we examine mucoid frequencies across several MyxoEE-6 timepoints to discriminate between the hypotheses that mucoids were increasing to fixation, stabilizing around equilibrium frequencies, or heading to loss toward the end of MyxoEE-6. In four focal coevolved prey populations, mucoids rose rapidly early in the experiment and then fluctuated within detectable minority frequency ranges through the end of MyxoEE-6, generating frequency dynamics suggestive of negative frequency-dependent selection. However, a competition experiment between mucoid and non-mucoid clones found a predation-specific advantage of the mucoid clone that was insensitive to frequency over the examined range, leaving the mechanism that maintains minority mucoidy unresolved. The advantage of mucoidy under predation was found to be associated with reduced population size after growth (productivity) in the absence of predators, suggesting a tradeoff between productivity and resistance to predation that we hypothesize may reverse mucoid vs non-mucoid fitness ranks within each MyxoEE-6 cycle. We also found that mucoidy was associated with diverse colony phenotypes and diverse candidate mutations primarily localized in the exopolysaccharide operon yjbEFGH. Collectively, our results show that selection from predatory bacteria can generate apparently stable sympatric phenotypic polymorphisms within coevolving prey populations and also allopatric diversity across populations by selecting for diverse mutations and colony phenotypes associated with mucoidy. More broadly, our results suggest that myxobacterial predation increases long-term diversity within natural microbial communities.

Slit-band gastropods (Pleurotomariida) from the Upper Triassic St. Cassian Formation and their diversity dynamics in the Triassic

The St. Cassian Formation, Italy, has yielded the most diverse marine invertebrate fauna known from the Triassic. A quarter of all described Triassic gastropod species has been reported from this formation. Most of the gastropod species from the St. Cassian Formation were erected in the 19th century and many of them are known only from their original figures and descriptions. The failure to study type specimens resulted in many erroneous identifications by subsequent authors. Here, we revise the slit band gastropods (Pleurotomariida) from the St. Cassian Formation—one of the major groups present in this formation. A total of 77 nominate Pleurotomariida species belonging to 29 genera and 11 families are present in the St. Cassian Formation which comprises approximately 14 % of the total nominate gastropod species of that formation. In addition, we revise several taxa that had been wrongly assigned to Pleurotomariida. As other gastropod clades, Pleurotomariida experienced a major extinction at the end-Permian mass extinction event. As in the Late Palaeozoic, their relative abundance in gastropod faunas continued to be 30 % in some Anisian faunas but decreased to 5–10 % afterwards. Their diversification at generic level became interrupted by an extinction event within the Carnian, probably by the Carnian Pluvial Event. As a result of their sluggish recovery compared to the other gastropod groups, their species diversity decreased from 26 % during the Permian to 18 % during the Triassic. Type specimens of the following genera are studied: Proteomphalus, Rhaphistomella, Temnotropis, Kittlidiscus, Stuorella, Schizogonium, Wortheniella, Bandelium, Lancedellia, Rinaldoella, Pseudowortheniella, Paleunema, Ampezzalina, Bandelastraea, Cheilotomona, Pseudoscalites, Delphinulopsis, and Cochlearia. Nine new pleurotomariidan genera are erected: Amplitomaria, Pseudoananias, Lineacingulum, Pressulasphaera, Cancellotomaria, Acutitomaria, Lineaetomaria, Nodocingulum, and Striacingulum. Eight new species are described: Schizogonium undae, Acutitomaria kustatscherae, Wortheniella klipsteini, Wortheniella paolofedelei, Rinaldoella tornata, Nodocingulum ernstkittli, Nodocingulum? turris, and Laubella subsulcata. Eoworthenia frydai is a new replacement name for Worthenia rarissima Barrande.

Manchukuo voices: re-interpreting a monumental space in Northeast China (1932–1945)

This article revisits Japan's empire-building in Northeast China through the construction of and reactions to the Daidō hiroba 大同広場 (Plaza of Great Unity) in Shinkyō, showing how Chinese and Japanese challenged the top-down attempt for building a totalitarian empire. These re-interpretations and definitions of Hiroba unveiled the diversity, dynamics, and complexity of Manchukuo society that cannot be fully grasped in a nation-state framework. Moreover, their voices challenged the previous depiction of such imperial monumental space as the physical materialization of imperial governmentality but a contested site where individuals challenged the official vision of Manchukuo. This article examines documents ranging from governmental documents to works of literature in both Chinese and Japanese. Compared to Japanese planners' vision of the Hiroba as a site of governmentality, visitors and local residents held differing interpretations of this space: some Japanese disapproved the attempt to reframe the urban space by a totalitarian regime, and many Chinese redefined the meaning of this “utopian” urban space to accord with their own tradition and everyday life.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii are the most speciose living vertebrate clade, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches, and there is no comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. Past studies typically show low levels of diversity in the Devonian with a substantial rise in the early Carboniferous in the aftermath of the end-Devonian mass extinction. However there are unresolved patterns reported for the later Carboniferous and Permian. In large part, these conflicts span from a lack of publicly-available occurrence data: actinopterygians are majorly underrepresented in the Paleobiology Database (PBDB), for example, obscuring patterns of diversity through time. This is exacerbated by major taxonomic problems pervading the Palaeozoic actinopterygian record. Innumerable taxa are lumped into wide-ranging families and poorly-formulated genera, with a vast number of described species concentrated in several particularly problematic ‘waste-basket’ genera. This taxonomic confusion feeds into a limited understanding of phylogenetic relationships. There is also a heavy sampling bias towards Europe and North America, with other regions underrepresented despite yielding important occurrences. Scrutiny of the extent to which spatial biases influence the record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effect of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway to both redescribe poorly defined taxa and describe taxa from underrepresented regions, helping address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity from those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.

Population Diversity, Dynamics, and Differentiation of Wheat Stripe Rust Pathogen Puccinia striiformis f. sp. tritici From 2010 to 2017 and Comparison With 1968 to 2009 in the United States

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious disease on wheat in the United States, especially after 2000. In the present study, 2,247 Pst isolates collected over all stripe rust epidemiological regions in the United States from 2010 to 2017 were genotyped at 14 simple sequence repeat (SSR) loci to investigate the population diversity, dynamics, and differentiation. A total of 1,454 multilocus genotypes (MLGs) were detected. In general, the populations in the west (regions 1–6) had more MLGs and higher diversities than the populations in the east (regions 7–12). The populations of 2010 and 2011 were more different from the other years. Genetic variation was higher among years than among regions, indicating the fast changes of the population. The divergence (Gst) was bigger between the west population and east population than among regions within either the west or east population. Gene flow was stronger among the regional populations in the east than in the west. Clustering analyses revealed 3 major molecular groups (MGs) and 10 sub-MGs by combining the genotypic data of 2010–2017 isolates with those of 1968–2009. MG1 contained both 1968–2009 isolates (23.1%) and 2010–2017 isolates (76.9%). MG2 had 99.4% of isolates from 1968–2009. MG3, which was the most recent and distinct group, had 99.1% of isolates from 2010–2017. Of the 10 sub-MGs, 5 (MG1-3, MG1-5, MG3-2, MG3-3, and MG3-4) were detected only from 2011 to 2017. The SSR genotypes had a moderate, but significant correlation (r = 0.325; p < 0.0001) with the virulence phenotype data. The standard index values of association (rbarD = 0.11) based on either regional or yearly populations suggest clonal reproduction. This study indicated high diversity, fast dynamics, and various levels of differentiation of the Pst population over the years and among epidemiological regions, and the results should be useful for managing wheat stripe rust.