Abstract. Initial conditions can generate differences in the biotic composition of spatially disjunct communities, but intense, large-scale perturbations have the potential to reduce or eliminate those historical differences. The latter possibility is of particular concern with respect to coral reefs, which have undergone dramatic changes in the last 25-30 years. This paper reports a case in which two reef systems with different biotic histories were recently perturbed to a single, novel state.We compared millennial-scale records of species dominance from reefs in Bahia Almirante, a coastal lagoon in northwestern Panama, to previously published records from reefs in the shelf lagoon of Belize. Reef cores extracted from Bahia Almirante at 5-10 m water depth revealed that the Panamanian reefs were persistently dissimilar from the Belizean reefs for at least 2000-3000 years prior to the last several decades. The Panamanian reefs were dominated continuously by branching finger corals, Porites spp. (primarily P. furcata). Shifts from the Ponfes-dominated state to dominance by other coral species were rare, were restricted to small areas, and lasted for decades to centuries. The Belizean reefs were dominated continuously by the staghorn coral Acropora cervicornis in the same depth range during the same period. Excursions from the Acropora-dominated state were again rare and spatially localized. Populations of Ac. cervicornis in the Belizean lagoon were nearly extirpated by an outbreak of white-band disease in the late 1980s, and changes in water quality were apparently detrimental to branching Porites in Bahia Almirante in recent decades. These large-scale perturbations caused the two reef systems to converge on a third, historically unprecedented state: dominance by the lettuce coral Agaricia tenuifolia. Ag. tenuifolia possesses life-history attributes and environmental tolerances that enabled it to become dominant in both disturbed ecosystems. Although the two phase shifts to Ag. tenuifolia differed in both their general mechanisms and specific causes, they had the effect of eliminating the salient difference in benthic composition between the Panamanian and Belizean reefs. The changes in species composition thus obliterated the influence of several thousand years of reef history.

Flow diversion and invasive species are two major threats to freshwater ecosystems, threats that restoration efforts attempt to redress. Yet, few restoration projects monitor whether removal of these threats improve target characteristics of the ecosystem. Fewer still have an appropriate experimental design from which causal inferences can be drawn as to the relative merits of removing exotic fish, restoring flow, or both. We used a dam decommissioning in Fossil Creek, Arizona, to compare responses of native fish to exotic fish removal and flow restoration, using a beforeafter-control-impact design with three impact treatments: flow restoration alone where exotics had not been present, flow restoration and exotic fish removal, and flow restoration where exotics remain and a control reach that was unaffected by restoration actions. We show that removal of exotic fish dramatically increased native fish abundance.Flow restoration also increased native fish abundance, but the effect was smaller than that from removing exotics. Flow restoration had no effect where exotic fish remained, although it may have had other benefits to the ecosystem. The cost to restore flow ($12 million) was considerably higher than that to eradicate exotics ($1.1 million). The long-term influence of flow restoration could increase, as travertine dams grow and re-shape the creek increasing habitat for native fish. But in the 2-year period considered here, the return on investment for extirpating exotics far exceeded that from flow restoration. Projects aimed to restore native fish by restoring flow should also consider the additional investment required to eradicate exotic fish.

Rooting phylogenies is critical for understanding evolution, yet the importance, intricacies and difficulties of rooting are often overlooked. For rooting, polymorphic characters among the group of interest (ingroup) must be compared to those of a relative (outgroup) that diverged before the last common ancestor (LCA) of the ingroup. Problems arise if an outgroup does not exist, is unknown, or is so distant that few characters are shared, in which case duplicated genes originating before the LCA can be used as proxy outgroups to root diverse phylogenies. Here, we describe a genome-wide expansion of this technique that can be used to solve problems at the other end of the evolutionary scale: where ingroup individuals are all very closely related to each other, but the next closest relative is very distant. We used shared orthologous single nucleotide polymorphisms (SNPs) from 10 whole genome sequences of Coxiella burnetii, the causative agent of Q fever in humans, to create a robust, but unrooted phylogeny. To maximize the number of characters informative about the rooting, we searched entire genomes for polymorphic duplicated regions where orthologs of each paralog could be identified so that the paralogs could be used to root the tree. Recent radiations, such as those of emerging pathogens, often pose rooting challenges due to a lack of ingroup variation and large genomic differences with known outgroups. Using a phylogenomic approach, we created a robust, rooted phylogeny for C. burnetii. [Coxiella burnetii; paralog SNPs; pathogen evolution; phylogeny; recent radiation; root; rooting using duplicated genes.]

We collected epidemiologic and molecular data from Burkholderia mallei isolates from equines in Punjab, Pakistan from 1999 through 2007. We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines.

The reintroduction of beaver (Castor canadensis) into arid and semi-arid rivers is receiving increasing management and conservation attention in recent years, yet very little is known about native versus non-native fish occupancy in beaver pond habitats. Streams of the American Southwest support a highly endemic, highly endangered native fish fauna and abundant non-native fishes, and here we investigated the hypothesis that beaver ponds in this region may lead to fish assemblages dominated by non-native species that favour slower-water habitat. We sampled fish assemblages within beaver ponds and within unimpounded lotic stream reaches in the mainstem and in tributaries of the free-flowing upper Verde River, Arizona, USA. Non-native fishes consistently outnumbered native species, and this dominance was greater in pond than in lotic assemblages. Few native species were recorded within ponds. Multivariate analysis indicated that fish assemblages in beaver ponds were distinct from those in lotic reaches, in both mainstem and tributary locations. Individual species driving this distinction included abundant nonnative green sunfish (Lepomis cyanellus) and western mosquitofish (Gambusia affinis) in pond sites, and native desert sucker (Catostomus clarkii) in lotic sites. Overall, this study provides the first evidence that, relative to unimpounded lotic habitat, beaver ponds in arid and semi-arid rivers support abundant non-native fishes; these ponds could thus serve as important non-native source areas and negatively impact co-occurring native fish populations.