Recruitment hotspots and bottlenecks mediate the distribution of corals on a Caribbean reef

Recruitment hotspots are locations where organisms are added to populations at high rates. On tropical reefs where coral abundance has declined, recruitment hotspots are important because they have the potential to promote population recovery. Around St. John, US Virgin Islands, coral recruitment at five sites revealed a hotspot that has persistent for 14 years. Recruitment created a hotspot in density of juvenile corals that was 600 m southeast of the recruitment hotspot. Neither hotspot led to increased coral cover, thus revealing the stringency of the demographic bottleneck impeding progression of recruits to adult sizes and preventing population growth. Recruitment hotspots in low-density coral populations are valuable targets for conservation and sources of corals for restoration.

Helicobacter pylori’s historical journey through Siberia and the Americas

The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.

A preliminary range-wide distribution model for the sacramento valley red fox

© 2017, Allen Press. All rights reserved. The Sacramento Valley red fox Vulpes vulpes patwin of California is a newly named subspecies recently found to be distinct both from other native red foxes and nearby introduced populations. The Sacramento Valley red fox experienced a historical demographic bottleneck resulting in a critically small genetic effective population size, causing concern over its current status and management requirements, yet little is known about its contemporary abundance, demographic trajectory, or habitat use. The hot, arid Sacramento Valley contrasts starkly in climate and physiography with the boreal habitats of other indigenous red foxes in western North America, indicating the need to obtain information specifically on the habitat requirements of this subspecies. A 3-y effort to locate reproductive den sites throughout the Sacramento Valley resulted in 42 independent dens, which we used to obtain preliminary information on habitat use and to develop a distribution model for this subspecies, and 28 Sacramento Valley red foxes killed by vehicles, which we used as independent data to test the models. Foxes were present significantly more than expected in grasslands and less than expected in wetlands and flooded agriculture and also tended to occur in proximity to human development, potentially as refuges from coyotes Canis latrans. We used Maxent to build predictive models. The best model, which incorporated vegetation/land-use classes and proximity to human development, identified 24% of the study area as predicted-presence habitat, which contained 76% of the den sites used to construct the model and 89% of independent locations used to test the model. Our model greatly narrowed the area over which foxes are predicted to occur and will facilitate future surveys to assess occupancy and ultimately abundance and population trends.

A preliminary range-wide distribution model for the sacramento valley red fox

© 2017, Allen Press. All rights reserved. The Sacramento Valley red fox Vulpes vulpes patwin of California is a newly named subspecies recently found to be distinct both from other native red foxes and nearby introduced populations. The Sacramento Valley red fox experienced a historical demographic bottleneck resulting in a critically small genetic effective population size, causing concern over its current status and management requirements, yet little is known about its contemporary abundance, demographic trajectory, or habitat use. The hot, arid Sacramento Valley contrasts starkly in climate and physiography with the boreal habitats of other indigenous red foxes in western North America, indicating the need to obtain information specifically on the habitat requirements of this subspecies. A 3-y effort to locate reproductive den sites throughout the Sacramento Valley resulted in 42 independent dens, which we used to obtain preliminary information on habitat use and to develop a distribution model for this subspecies, and 28 Sacramento Valley red foxes killed by vehicles, which we used as independent data to test the models. Foxes were present significantly more than expected in grasslands and less than expected in wetlands and flooded agriculture and also tended to occur in proximity to human development, potentially as refuges from coyotes Canis latrans. We used Maxent to build predictive models. The best model, which incorporated vegetation/land-use classes and proximity to human development, identified 24% of the study area as predicted-presence habitat, which contained 76% of the den sites used to construct the model and 89% of independent locations used to test the model. Our model greatly narrowed the area over which foxes are predicted to occur and will facilitate future surveys to assess occupancy and ultimately abundance and population trends.

Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox

Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’

Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa

Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500–700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.

A Preliminary Range-Wide Distribution Model for the Sacramento Valley Red Fox

The Sacramento Valley red fox Vulpes vulpes patwin of California is a newly named subspecies recently found to be distinct both from other native red foxes and nearby introduced populations. The Sacramento Valley red fox experienced a historical demographic bottleneck resulting in a critically small genetic effective population size, causing concern over its current status and management requirements, yet little is known about its contemporary abundance, demographic trajectory, or habitat use. The hot, arid Sacramento Valley contrasts starkly in climate and physiography with the boreal habitats of other indigenous red foxes in western North America, indicating the need to obtain information specifically on the habitat requirements of this subspecies. A 3-y effort to locate reproductive den sites throughout the Sacramento Valley resulted in 42 independent dens, which we used to obtain preliminary information on habitat use and to develop a distribution model for this subspecies, and 28 Sacramento Valley red foxes killed by vehicles, which we used as independent data to test the models. Foxes were present significantly more than expected in grasslands and less than expected in wetlands and flooded agriculture and also tended to occur in proximity to human development, potentially as refuges from coyotes Canis latrans. We used Maxent to build predictive models. The best model, which incorporated vegetation/land-use classes and proximity to human development, identified 24% of the study area as predicted-presence habitat, which contained 76% of the den sites used to construct the model and 89% of independent locations used to test the model. Our model greatly narrowed the area over which foxes are predicted to occur and will facilitate future surveys to assess occupancy and ultimately abundance and population trends.

Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network

Demographic bottlenecks that occur when populations fluctuate in size erode genetic diversity, but that diversity can be recovered through immigration. Connectivity among populations and habitat patches in the landscape enhances immigration and should in turn facilitate recovery of genetic diversity after a sudden reduction in population size. For the conservation of genetic diversity, it may therefore be particularly important to maintain connectivity in the face of factors that increase demographic instability, such as climate change. However, a direct link between connectivity and recovery of genetic diversity after a demographic bottleneck has not been clearly demonstrated in an empirical system. Here, we show that connectivity of habitat patches in the landscape contributes to the maintenance of genetic diversity after a demographic bottleneck. We were able to monitor genetic diversity in a network of populations of the alpine butterfly, Parnassius smintheus, before, during, and after a severe reduction in population size that lasted two generations. We found that allelic diversity in the network declined after the demographic bottleneck but that less allelic diversity was lost from populations occupying habitat patches with higher connectivity. Furthermore, the effect of connectivity on allelic diversity was important during the demographic recovery phase. Our results demonstrate directly the ability of connectivity to mediate the rescue of genetic diversity in a natural system.