Phylogeography and population genomics of a lotic water beetle across a complex tropical landscape

The habitat template concept applied to a freshwater system indicates that lotic species, or those which occupy permanent habitats along stream courses, are less dispersive than lentic species, or those that occur in more ephemeral aquatic habitats. Thus, populations of lotic species will be more structured than those of lentic species. Stream courses include both flowing water and small, stagnant microhabitats that can provide refuge when streams are low. Many species occur in these microhabitats but remain poorly studied. Here, we present population genetic data for one such species, the tropical diving beetle Exocelina manokwariensis (Dytiscidae), sampled from six localities along a ~300 km transect across the Birds Head Peninsula of New Guinea. Molecular data from both mitochondrial (CO1 sequences) and nuclear (ddRAD loci) regions document fine‐scale population structure across populations that are ~45 km apart. Our results are concordant with previous phylogenetic and macroecological studies that applied the habitat template concept to aquatic systems. This study also illustrates that these diverse but mostly overlooked microhabitats are promising study systems in freshwater ecology and evolutionary biology. With the advent of next‐generation sequencing, fine‐scale population genomic studies are feasible for small nonmodel organisms to help illuminate the effect of habitat stability on species’ natural history, population structure and geographic distribution.     

Ecosystem‐level effects of keystone species reintroduction: a literature review

The keystone species concept was introduced in 1969 in reference to top‐down regulation of communities by predators, but has expanded to include myriad species at different trophic levels. Keystone species play disproportionately large, important roles in their ecosystems, but human‐wildlife conflicts often drive population declines. Population declines have resulted in the necessity of keystone species reintroduction; however, studies of such reintroductions are rare. We conducted a literature review and found only 30 peer‐reviewed journal articles that assessed reintroduced populations of keystone species, and only 11 of these assessed ecosystem‐level effects following reintroduction. Nine of 11 publications assessing ecosystem‐level effects found evidence of resumption of keystone roles; however, these publications focus on a narrow range of species. We highlight the deficit of peer‐reviewed literature on keystone species reintroductions, and draw attention to the need for assessment of ecosystem‐level effects so that the presence, extent, and rate of ecosystem restoration driven by keystone species can be better understood.     

A biogeographical perspective on the variation in mouse lemur density throughout Madagascar

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Quantifying the links between land use and population growth rate in a declining farmland bird

Land use is likely to be a key driver of population dynamics of species inhabiting anthropogenic landscapes, such as farmlands. Understanding the relationships between land use and variation in population growth rates is therefore critical for the management of many farmland species. Using 24 years of data of a declining farmland bird in an integrated population model, we examined how spatiotemporal variation in land use (defined as habitats with “Short” and “Tall” ground vegetation during the breeding season) and habitat‐specific demographic parameters relates to variation in population growth taking into account individual movements between habitats. We also evaluated contributions to population growth using transient life table response experiments which gives information on contribution of past variation of parameters and real‐time elasticities which suggests future scenarios to change growth rates. LTRE analyses revealed a clear contribution of Short habitats to the annual variation in population growth rate that was mostly due to fledgling recruitment, whereas there was no evidence for a contribution of Tall habitats. Only 18% of the variation in population growth was explained by the modeled local demography, the remaining variation being explained by apparent immigration (i.e., the residual variation). We discuss potential biological and methodological reasons for high contributions of apparent immigration in open populations. In line with LTRE analysis, real‐time elasticity analysis revealed that demographic parameters linked to Short habitats had a stronger potential to influence population growth rate than those of Tall habitats. Most particularly, an increase of the proportion of Short sites occupied by Old breeders could have a distinct positive impact on population growth. High‐quality Short habitats such as grazed pastures have been declining in southern Sweden. Converting low‐quality to high‐quality habitats could therefore change the present negative population trend of this, and other species with similar habitat requirements.     

Population structure leads to male‐biased population sex ratios under environmental sex determination

Spatial structure has been shown to favor female‐biased sex allocation, but current theory fails to explain male biases seen in many taxa, particularly those with environmental sex determination (ESD). We present a theory and accompanying individual‐based simulation model that demonstrates how population structure leads to male‐biased population sex ratios under ESD. Our simulations agree with earlier work showing that the high productivity of female‐producing habitats creates a net influx of sex‐determining alleles into male‐producing habitats, causing larger sex ratio biases, and lower productivity in male‐producing environments (Harts et al. 2014). In contrast to previous findings, we show that male‐biasing habitats disproportionately impact the global sex ratio, resulting in stable male‐biased population sex ratios under ESD. The failure to detect a male bias in earlier work can be attributed to small subpopulation sizes leading to local mate competition, a condition unlikely to be met in most ESD systems. Simulations revealed that consistent male biases are expected over a wide range of population structures, environmental conditions, and genetic architectures of sex determination, with male excesses as large as 30 percent under some conditions. Given the ubiquity of genetic structure in natural populations, we predict that modest, enduring male biased allocation should be common in ESD species, a pattern consistent with reviews of ESD sex ratios.     

Population dynamics of three songbird species in a nestbox population in Central Europe show effects of density,climate and competitive interactions

Unravelling the contributions of density‐dependent and density‐independent factors in determining species population dynamics is a challenge, especially if the two factors interact. One approach is to apply stochastic population models to long‐term data, yet few studies have included interactions between density‐dependent and density‐independent factors, or explored more than one type of stochastic population model. However, both are important because model choice critically affects inference on population dynamics and stability. Here, we used a multiple models approach and applied log‐linear and non‐linear stochastic population models to time series (spanning 29 years) on the population growth rates of Blue Tits Cyanistes caeruleus, Great Tits Parus major and Pied Flycatchers Ficedula hypoleuca breeding in two nestbox populations in southern Germany. We focused on the roles of climate conditions and intra‐ and interspecific competition in determining population growth rates. Density dependence was evident in all populations. For Blue Tits in one population and for Great Tits in both populations, addition of a density‐independent factor improved model fit. At one location, Blue Tit population growth rate increased following warmer winters, whereas Great Tit population growth rates decreased following warmer springs. Importantly, Great Tit population growth rate also decreased following years of high Blue Tit abundance, but not vice versa. This finding is consistent with asymmetric interspecific competition and implies that competition could carry over to influence population dynamics. At the other location, Great Tit population growth rate decreased following years of high Pied Flycatcher abundance but only when Great Tit population numbers were low, illustrating that the roles of density‐dependent and density‐independent factors are not necessarily mutually exclusive. The dynamics of this Great Tit population, in contrast to the other populations, were unstable and chaotic, raising the question of whether interactions between density‐dependent and density‐independent factors play a role in determining the (in) stability of the dynamics of species populations.     

Refining predictions of population decline at species' rear edges

According to broad‐scale application of biogeographical theory, widespread retractions of species' rear edges should be seen in response to ongoing climate change. This prediction rests on the assumption that rear edge populations are “marginal” since they occur at the limit of the species' ecological tolerance and are expected to decline in performance as climate warming pushes them to extirpation. However, conflicts between observations and predictions are increasingly accumulating and little progress has been made in explaining this disparity. We argue that a revision of the concept of marginality is necessary, together with explicit testing of population decline, which is increasingly possible as data availability improves. Such action should be based on taking the population perspective across a species' rear edge, encompassing the ecological, geographical and genetic dimensions of marginality. Refining our understanding of rear edge populations is essential to advance our ability to monitor, predict and plan for the impacts of environmental change on species range dynamics.     

The fin whale Balaenoptera physalus (L. 1758) in the Mediterranean Sea

1. The ecology and status of fin whales Balaenoptera physalus in the Mediterranean Sea is reviewed. The species’ presence, morphology, distribution, movements, population structure, ecology and behaviour in this semi‐enclosed marine region are summarized, and the review is complemented with original, previously unpublished data. 2. Although the total size of the fin whale population in the Mediterranean is unknown, an estimate for a portion of the western basin, where most of the whales are known to live, was approximately 3500 individuals. High whale densities, comparable to those found in rich oceanic habitats, were found in well‐defined areas of high productivity. Most whales concentrate in the Ligurian‐Corsican‐Provençal Basin, where their presence is particularly noticeable during summer; however, neither their movement patterns throughout the region nor their seasonal cycle are clear. 3. Based on genetic studies, fin whales from the Mediterranean Sea are distinct from North Atlantic conspecifics, and may constitute a resident population, separate from those of the North Atlantic, despite the species’ historical presence in the Strait of Gibraltar. Fin whales are known to calve in the Mediterranean, with births peaking in November but occurring at lower rates throughout the year. They feed primarily on krill Meganyctiphanes norvegica which they capture by diving to depths in excess of 470 m. It is suggested that the extensive vertical migratory behaviour of its main prey may have influenced the social ecology of this population. 4. Known causes of mortality and threats, including collisions with vessels, entanglement in fishing gear, deliberate killing, disturbance, pollution and disease, are listed and discussed in view of the implementation of appropriate conservation measures to ensure the species’ survival in the region.     

Intragenomic conflict produces sex ratio dynamics that favor maternal sex ratio distorters

Maternal sex ratio distorters (MSDs) are selfish elements that enhance their transmission by biasing their host's sex allocation in favor of females. While previous models have predicted that the female‐biased populations resulting from sex ratio distortion can benefit from enhanced productivity, these models neglect Fisherian selection for nuclear suppressors, an unrealistic assumption in most systems. We used individual‐based computer simulation modeling to explore the intragenomic conflict between sex ratio distorters and their suppressors and explored the impacts of these dynamics on population‐level competition between species characterized by MSDs and those lacking them. The conflict between distorters and suppressors was capable of producing large cyclical fluctuations in the population sex ratio and reproductive rate. Despite fitness costs associated with the distorters and suppressors, MSD populations often exhibited enhanced productivity and outcompeted non‐MSD populations in single and multiple‐population competition simulations. Notably, the conflict itself is beneficial to the success of populations, as sex ratio oscillations limit the competitive deficits associated with prolonged periods of male rarity. Although intragenomic conflict has been historically viewed as deleterious to populations, our results suggest that distorter–suppressor conflict can provide population‐level advantages, potentially helping to explain the persistence of sex ratio distorters in a range of taxa.     

Identification of source‐sink dynamics in mountain lions of the Great Basin

Natural and anthropogenic boundaries have been shown to affect population dynamics and population structure for many species with movement patterns at the landscape level. Understanding population boundaries and movement rates in the field for species that are cryptic and occur at low densities is often extremely difficult and logistically prohibitive; however genetic techniques may offer insights that have previously been unattainable. We analysed thirteen microsatellite loci for 739 mountain lions (Puma concolor) using muscle tissue samples from individuals in the Great Basin throughout Nevada and the Sierra Nevada mountain range to test the hypothesis that heterogeneous hunting pressure results in source‐sink dynamics at the landscape scale. We used a combination of non‐spatial and spatial model‐based Bayesian clustering methods to identify genetic populations. We then used a recently developed Bayesian multilocus genotyping method to estimate asymmetrical rates of contemporary movement between those subpopulations and to identify source and sink populations. We identified two populations at the highest level of genetic structuring with a total of five subpopulations in the Great Basin of Nevada and the Sierra Nevada range. Our results suggest that source‐sink dynamics occur at landscape scales for wide‐ranging species, such as mountain lions, and that source populations may be those that are under relatively less hunting pressure and that occupy refugia.     

Top–down limits on prey populations may be more severe in larger prey species,despite having fewer predators

Variation in the vulnerability of herbivore prey to predation is linked to body size, yet whether this relationship is size‐nested or size‐partitioned remains debated. If size‐partitioned, predators would be focused on prey within their preferred prey size range. If size‐nested, smaller prey species should become increasingly more vulnerable because increasingly more predators are capable of catching them. Yet, whether either of these strategies manifests in top–down prey population limitation would depend both on the number of potential predator species as well as the total mortality imposed. Here we use a rare ecosystem scale ‘natural experiment’ comparing prey population dynamics between a period of intense predator persecution and hence low predator densities and a period of active predator protection and population recovery. We use three decades of data on herbivore abundance and distribution to test the role of predation as a mechanism of population limitation among prey species that vary widely in body size. Notably, we test this within one of the few remaining systems where a near‐full suite of megaherbivores occur in high density and are thus able to include a thirtyfold range in herbivore body size gradient. We test whether top–down limitation on prey species of particular body size leads to compositional shifts in the mammalian herbivore community. Our results support both size‐nested and size‐partitioning predation but suggest that the relative top–down limiting impact on prey populations may be more severe for intermediate sized species, despite having fewer predators than small species. In addition we show that the gradual recovery of predator populations shifted the herbivore community assemblage towards large‐bodied species and has led to a community that is strongly dominated by large herbivore biomass.     

Life‐history predicts past and present population connectivity in two sympatric sea stars

Life‐history traits, especially the mode and duration of larval development, are expected to strongly influence the population connectivity and phylogeography of marine species. Comparative analysis of sympatric, closely related species with differing life histories provides the opportunity to specifically investigate these mechanisms of evolution but have been equivocal in this regard. Here, we sample two sympatric sea stars across the same geographic range in temperate waters of Australia. Using a combination of mitochondrial DNA sequences, nuclear DNA sequences, and microsatellite genotypes, we show that the benthic‐developing sea star, Parvulastra exigua, has lower levels of within‐ and among‐population genetic diversity, more inferred genetic clusters, and higher levels of hierarchical and pairwise population structure than Meridiastra calcar, a species with planktonic development. While both species have populations that have diverged since the middle of the second glacial period of the Pleistocene, most P. exigua populations have origins after the last glacial maxima (LGM), whereas most M. calcar populations diverged long before the LGM. Our results indicate that phylogenetic patterns of these two species are consistent with predicted dispersal abilities; the benthic‐developing P. exigua shows a pattern of extirpation during the LGM with subsequent recolonization, whereas the planktonic‐developing M. calcar shows a pattern of persistence and isolation during the LGM with subsequent post‐Pleistocene introgression.     

Loss of genetic diversity,recovery and allele surfing in a colonizing parasite,Geomydoecus aurei

Understanding the genetic consequences of changes in species distributions has wide‐ranging implications for predicting future outcomes of climate change, for protecting threatened or endangered populations and for understanding the history that has led to current genetic patterns within species. Herein, we examine the genetic consequences of range expansion over a 25‐year period in a parasite (Geomydoecus aurei) that is in the process of expanding its geographic range via invasion of a novel host. By sampling the genetics of 1,935 G. aurei lice taken from 64 host individuals collected over this time period using 12 microsatellite markers, we test hypotheses concerning linear spatial expansion, genetic recovery time and allele surfing. We find evidence of decreasing allelic richness (AR) with increasing distance from the source population, supporting a linear, stepping stone model of spatial expansion that emphasizes the effects of repeated bottleneck events during colonization. We provide evidence of post‐bottleneck genetic recovery, with average AR of infrapopulations increasing about 30% over the 225‐generation span of time observed directly in this study. Our estimates of recovery rate suggest, however, that recovery has plateaued and that this population may not reach genetic diversity levels of the source population without further immigration from the source population. Finally, we employ a grid‐based sampling scheme in the region of ongoing population expansion and provide empirical evidence for the power of allele surfing to impart genetic structure on a population, even under conditions of selective neutrality and in a place that lacks strong barriers to gene flow.     

Species pool size and invasibility of island communities: a null model of sampling effects

The success of alien species on oceanic islands is considered to be one of the classic observed patterns in ecology. Explanations for this pattern are based on lower species richness on islands and the lower resistance of species‐poor communities to invaders, but this argument needs re‐examination. The important difference between islands and mainland is in the size of species pools, not in local species richness; invasibility of islands should therefore be addressed in terms of differences in species pools. Here I examine whether differences in species pools can affect invasibility in a lottery model with pools of identical native and exotic species. While in a neutral model with all species identical, invasibility does not depend on the species pool, a model with non‐zero variation in population growth rates predicts higher invasibility of communities of smaller pools. This is because of species sampling; drawing species from larger pools increases the probability that an assemblage will include fast growing species. Such assemblages are more likely to exclude random invaders. This constitutes a mechanism through which smaller species pools (such as those of isolated islands) can directly underlie differences in invasibility.     

Population status of Andean Condors in central and southern Bolivia

Andean Condors (Vultur gryphus) are a Near Threatened species that was formerly distributed along the entire length of the Andes from western Venezuela to Tierra del Fuego. Populations have been severely reduced north of Peru, but several thousand Andean Condors still exist in the southern portion of their range in Argentina and Chile. Little is known, however, about the size of the Andean Condor population in the central part of their range in Peru and Bolivia. From June to September 2012, we used feeding stations to attract Andean Condors and estimate the size and structure of the population in the eastern Andes of central and southern Bolivia. We estimated a minimum population of 253 condors, an adult male‐to‐female ratio of 1:0.6, an immature male‐to‐female ratio of 1:0.9, and an adult‐to‐immature ratio of 1:1.1. At our five survey areas, estimated abundance ranged from 15 to 100 condors per area. Males outnumbered females in three areas and the opposite was true in two areas. Our estimated adult‐to‐immature ratio, overall and in each area, suggests that the populations could be reproducing at a high rate. As previously observed in other Andean Condor populations, skewed sex ratios could be associated with differences between sexes and age classes in habitat selection. Although our results suggest that Bolivian populations of Andean Condors are still reasonably large, population monitoring is urgently needed, including use of feeding stations throughout the entire Bolivian range of the species and intensive searches for roosting and nesting sites.     

Modelling climate‐change‐induced nonlinear thresholds in cephalopod population dynamics

A significant global challenge lies in our current inability to anticipate, and therefore prepare for, critical ecological thresholds (i.e. tipping points in ecosystems). This deficit stems largely from an inadequate understanding of the many complex interactions between species and the environment at the ecosystem level, and the paucity of mechanistic models relating environment to population dynamics at the species level. In marine ecosystems, abundant, short‐lived and fast‐growing species such as anchovies or squids, consistently function as ‘keystone’ groups whose population dynamics affect entire ecosystems. Increasing exploitation coupled with climate change impacts has the potential to affect these ecological groups and consequently, the entire marine ecosystem. There are currently very few models that predict the impact of climate change on these keystone groups. Here we use a combination of individual‐based bioenergetics and stage‐structured population models to characterize the fundamental capacity of cephalopods to respond to climate change. We demonstrate the potential for, and mechanisms behind, two unfavourable climate‐change‐induced thresholds in future population dynamics. Although one threshold was the direct consequence of a decrease in incubation time caused by ocean warming, the other threshold was linked to survivorship, implying the possibility of management through a modification of fishing mortality. Additional substantive changes in phenology were also predicted, with a possible loss in population resilience. Our results demonstrate the feasibility of predicting complex nonlinear dynamics with a reasonably simplistic mechanistic model, and highlight the necessity of developing such approaches for other species if attempts to moderate the impact of climate change on natural resources are to be effective.     

DYNAMICS OF POLYPLOID FORMATION IN TRAGOPOGON (ASTERACEAE): RECURRENT FORMATION,GENE FLOW,AND POPULATION STRUCTURE

Polyploidy is a major feature of angiosperm evolution and diversification. Most polyploid species have formed multiple times, yet we know little about the genetic consequences of recurrent formations. Among the clearest examples of recurrent polyploidy are Tragopogon mirus and T. miscellus (Asteraceae), each of which has formed repeatedly in the last ～80 years from known diploid progenitors in western North America. Here, we apply progenitor‐specific microsatellite markers to examine the genetic contributions to each tetraploid species and to assess gene flow among populations of independent formation. These data provide fine‐scale resolution of independent origins for both polyploid species. Importantly, multiple origins have resulted in considerable genetic variation within both polyploid species; however, the patterns of variation detected in the polyploids contrast with those observed in extant populations of the diploid progenitors. The genotypes detected in the two polyploid species appear to represent a snapshot of historical population structure in the diploid progenitors, rather than modern diploid genotypes. Our data also indicate a lack of gene flow among polyploid plants of independent origin, even when they co‐occur, suggesting potential reproductive barriers among separate lineages in both polyploid species.     

Atypical panmixia in a European dolphin species (Delphinus delphis): implications for the evolution of diversity across oceanic boundaries

Despite the scarcity of geographical barriers in the ocean environment, delphinid cetaceans often exhibit marked patterns of population structure on a regional scale. The European coastline is a prime example, with species exhibiting population structure across well‐defined environmental boundaries. Here we undertake a comprehensive population genetic study on the European common dolphin (Delphinus delphis, based on 492 samples and 15 loci) and establish that this species shows exceptional panmixia across most of the study range. We found differentiation only between the eastern and western Mediterranean, consistent with earlier studies, and here use approximate Bayesian computations to explore different scenarios to explain the observed pattern. Our results suggest that a recent population bottleneck likely contributed significantly to the differentiation of the Eastern Mediterranean population (in Greek waters). This interpretation is consistent with independent census data that suggest a sharp population decline in the recent past. The implication is that an unperturbed population may currently show panmixia across the full study range. This exception to the more typical pattern of population structure seen for other regional dolphin species (and for common dolphin populations elsewhere in the world) suggests particular ecological or life‐history traits distinct to this species in European waters.     

Threats and biodiversity in the mediterranean biome

Aim Global conservation assessments recognize the mediterranean biome as a priority for the conservation of the world's biodiversity. To better direct future conservation efforts in the biome, an improved understanding of the location, magnitude and trend of key threats and their relationship with species of conservation importance is needed. Location Mediterranean‐climate regions in California‐Baja California, Chile, South Africa, Australia and the Mediterranean Basin. Methods We undertook a systematic, pan‐regional assessment of threats in the mediterranean biome including human population density, urban area and agriculture. To realize the full implications of these threats on mediterranean biodiversity, we examined their relationship with species of conservation concern: threatened mammals at the global scale and threatened plants at the subecoregional scale in California, USA. Results Across the biome, population density and urban area increased by 13% and agriculture by 1% between 1990 and 2000. Both population density and urban area were greatest in California‐Baja California and least in Australia while, in contrast, agriculture was greatest in Australia and least in California‐Baja California. In all regions lowlands were most affected by the threats analysed, with the exception of population density in the Chilean matorral. Threatened species richness had a significant positive correlation with population density at global and subecoregional scales, while threatened species were found to increase with the amount of urban area and decrease as the amount of natural area and unfragmented core area increased. Main conclusions Threats to mediterranean biodiversity have increased from 1990 to 2000, although patterns vary both across and within the five regions. The need for future conservation efforts is further underlined by the positive correlation between species of conservation concern and the increase in population density over the last decade. Challenges to reducing threats extend beyond those analysed to include human–environmental interactions and their synergistic effects, such as urbanization and invasive species and wildfires.     

Effectiveness of a protected areas network in the conservation of Tamarindus indica (Leguminosea–Caesalpinioideae) in Benin

In the absence of effective conservation of its wild relatives, exploitation of a species could lead to genetic depletion. Research on how well do protected areas contribute to the conservation of plant species subject to human exploitation is still limited. The potential niche of Tamarindus indica (tamarind) was evaluated and the contribution of the protected areas network (PAN) of Benin to its conservation was assessed. The maximum entropy approach was used to model the ecological niche of the species, and forest inventories were used to address its population structure. To test its effectiveness, the PAN map was overlapped with the habitat suitability map of the species, and its population structures in protected versus unprotected areas were compared. Tamarindus natural populations were confined to the Sudanian and Sudano‐Guinean regions. The species populations in the Sudanian region appeared well represented in protected areas in contrast to those in the Sudano‐Guinean region. Results showed a positive effect of protected areas on juvenile density but a weak effect on adult density and current size‐class distribution. Protection seemed to be unlikely to ensure the long‐term persistence of the species. Cryopreservation, assisted recruitment and artificial enrichment of tamarind stands are recommended to ensure the long‐term persistence of the species.