Guinevere O. U. Wogan

Has the Earth’s sixth mass extinction already arrived?

Palaeontologists characterize mass extinctions as times when the Earth loses more than three-quarters of its species in a geologically short interval, as has happened only five times in the past 540 million years or so. Biologists now suggest that a sixth mass extinction may be under way, given the known species losses over the past few centuries and millennia. Here we review how differences between fossil and modern data and the addition of recently available palaeontological information influence our understanding of the current extinction crisis. Our results confirm that current extinction rates are higher than would be expected from the fossil record, highlighting the need for effective conservation measures.

Genetic evidence for a high diversity and wide distribution of endemic strains of the pathogenic chytrid fungus Batrachochytrium dendrobatidis in wild Asian amphibians.

Population declines and extinctions of amphibians have been attributed to the chytrid fungus Batrachochytrium dendrobatidis (Bd), especially one globally emerging recombinant lineage (‘Bd‐GPL’). We used PCR assays that target the ribosomal internal transcribed spacer region (ITS) of Bd to determine the prevalence and genetic diversity of Bd in South Korea, where Bd is widely distributed but is not known to cause morbidity or mortality in wild populations. We isolated Korean Bd strains from native amphibians with low infection loads and compared them to known worldwide Bd strains using 19 polymorphic SNP and microsatellite loci. Bd prevalence ranged between 12.5 and 48.0%, in 11 of 17 native Korean species, and 24.7% in the introduced bullfrog Lithobates catesbeianus. Based on ITS sequence variation, 47 of the 50 identified Korean haplotypes formed a group closely associated with a native Brazilian Bd lineage, separated from the Bd‐GPL lineage. However, multilocus genotyping of three Korean Bd isolates revealed strong divergence from both Bd‐GPL and the native Brazilian Bd lineages. Thus, the ITS region resolves genotypes that diverge from Bd‐GPL but otherwise generates ambiguous phylogenies. Our results point to the presence of highly diversified endemic strains of Bd across Asian amphibian species. The rarity of Bd‐GPL‐associated haplotypes suggests that either this lineage was introduced into Korea only recently or Bd‐GPL has been outcompeted by native Bd strains. Our results highlight the need to consider possible complex interactions among native Bd lineages, Bd‐GPL and their associated amphibian hosts when assessing the spread and impact of Bd‐GPL on worldwide amphibian populations.

Natural history collections as windows on evolutionary processes.

Natural history collections provide an immense record of biodiversity on Earth. These repositories have traditionally been used to address fundamental questions in biogeography, systematics and conservation. However, they also hold the potential for studying evolution directly. While some of the best direct observations of evolution have come from long‐term field studies or from experimental studies in the laboratory, natural history collections are providing new insights into evolutionary change in natural populations. By comparing phenotypic and genotypic changes in populations through time, natural history collections provide a window into evolutionary processes. Recent studies utilizing this approach have revealed some dramatic instances of phenotypic change over short timescales in response to presumably strong selective pressures. In some instances, evolutionary change can be paired with environmental change, providing a context for potential selective forces. Moreover, in a few cases, the genetic basis of phenotypic change is well understood, allowing for insight into adaptive change at multiple levels. These kinds of studies open the door to a wide range of previously intractable questions by enabling the study of evolution through time, analogous to experimental studies in the laboratory, but amenable to a diversity of species over longer timescales in natural populations.

Prelude to the Anthropocene: Two new North American Land Mammal Ages (NALMAs)

Human impacts have left and are leaving distinctive imprints in the geological record. Here we show that in North America, the human-caused changes evident in the mammalian fossil record since c. 14,000 years ago are as pronounced as earlier faunal changes that subdivide Cenozoic epochs into the North American Land Mammal Ages (NALMAs). Accordingly, we define two new North American Land Mammal Ages, the Santarosean and the Saintagustinean, which subdivide Holocene time and complete a biochronologic system that has proven extremely useful in dating terrestrial deposits and in revealing major features of faunal change through the past 66 million years. The new NALMAs highlight human-induced changes to the Earth system, and inform the debate on whether or not defining an Anthropocene epoch is justified, and if so, when it began.

Life History Traits and Niche Instability Impact Accuracy and Temporal Transferability for Historically Calibrated Distribution Models of North American Birds

A primary assumption of environmental niche models (ENMs) is that models are both accurate and transferable across geography or time; however, recent work has shown that models may be accurate but not highly transferable. While some of this is due to modeling technique, individual species ecologies may also underlie this phenomenon. Life history traits certainly influence the accuracy of predictive ENMs, but their impact on model transferability is less understood. This study investigated how life history traits influence the predictive accuracy and transferability of ENMs using historically calibrated models for birds. In this study I used historical occurrence and climate data (1950-1990s) to build models for a sample of birds, and then projected them forward to the ‘future’ (1960-1990s). The models were then validated against models generated from occurrence data at that ‘future’ time. Internal and external validation metrics, as well as metrics assessing transferability, and Generalized Linear Models were used to identify life history traits that were significant predictors of accuracy and transferability. This study found that the predictive ability of ENMs differs with regard to life history characteristics such as range, migration, and habitat, and that the rarity versus commonness of a species affects the predicted stability and overlap and hence the transferability of projected models. Projected ENMs with both high accuracy and transferability scores, still sometimes suffered from over- or under- predicted species ranges. Life history traits certainly influenced the accuracy of predictive ENMs for birds, but while aspects of geographic range impact model transferability, the mechanisms underlying this are less understood.

Deep genetic structure and ecological divergence in a widespread human commensal toad

The Asian common toad (Duttaphrynus melanostictus) is a human commensal species that occupies a wide variety of habitats across tropical Southeast Asia. We test the hypothesis that genetic variation in D. melanostictus is weakly associated with geography owing to natural and human-mediated dispersal facilitated by its commensal nature. Phylogenetic and population genetic analyses of mitochondrial and nuclear DNA sequence variation, and predictive species distribution modelling, unexpectedly recovered three distinct evolutionary lineages that differ genetically and ecologically, corresponding to the Asian mainland, coastal Myanmar and the Sundaic islands. The persistence of these three divergent lineages, despite ample opportunities for recent human-mediated and geological dispersal, suggests that D. melanostictus actually consists of multiple species, each having narrower geographical ranges and ecological niches, and higher conservation value, than is currently recognized. These findings also have implications for the invasion potential of this human commensal elsewhere, such as in its recently introduced ranges on the islands of Borneo, Sulawesi, Seram and Madagascar.

Development and characterization of thirteen microsatellite markers for the Fiscal Flycatcher (Sigelus silens) for use in phylogeographic and landscape genetics research

ABSTRACTThe Fiscal Flycatcher, Sigelus silens, is the only representative of a monotypic genus, endemic to Southern Africa, and may represent two cryptic species. Here we describe the development of thirteen microsatellite markers, and characterize polymorphism for each one. We found that all but one of our 13 loci were highly variable, each having five or more alleles. This suggests that these markers will have high variability across the species range and will be of utility in understanding the extent of gene flow among populations.

Microsatellite markers for the Cape Robin-Chat (Cossypha caffra) and the Red-capped Robin-Chat (Cossypha natalensis) for use in demographic and landscape genetics analyses

The Robin-chats (Muscicapidae: Cossypha) are distributed across sub-saharan Africa with many species restricted to small fragments of Afromontane forest. Several species have decreasing population trends, so demographic data and landscape genetic data for these species will be essential for conservation management. Here we develop 23 microsatellite markers for two species of Cossypha (C. caffra and C. natalensis), characterize polymorphism, and cross-amplify a subset of loci. We demonstrate that most markers have high information content with many alleles suggesting that these markers will be useful for assessing population dynamics and demography. Several loci cross-amplified between species and retained high polymorphism, indicating that these loci will likely be of high utility for many species of African Robins.

Toxic Toad Invasion of Wallacea: a Biodiversity Hotspot Characterized by Extraordinary Endemism

(a) A map of Wallacea showing islands invaded by Duttaphrynus melanostictus in red, islands inhabited by Varanus komodoensis in blue, and localities of genetic samples in yellow points. (b) A D. melanostictus from Lombok Island. (c) Environmental niche model for the Sunda Islands clade of D. melanostictus projected into Wallacea. Green color indicates very high suitability, yellow color indicates high suitability, and orange color indicates moderate suitability.

Niche divergence builds the case for ecological speciation in skinks of the Plestiodon skiltonianus species complex

Abstract Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate‐based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by‐product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size‐divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.