Genetic data in population viability analysis: case studies with ambystomatid salamanders

Population viability analysis of common marsupials, Didelphis marsupialis and Didelphis virginiana, in a scenario of constant loss of native vegetation

We studied the population viability of two common marsupials, Didelphis marsupialis and Didelphis virginiana, based on field data and published ecological and genetic information. Using the VORTEX v. 10. 2.6 program, a 100-year simulation was performed with 1000 iterations for five populations of D. marsupialis and six of D. virginiana. A low probability of extinction was observed in both species, particularly for D. virginiana (0.000–0.007). Population size is higher considering a metapopulation dynamics approach versus individual populations for the two marsupials: 498.25 individuals for D. marsupialis and 367.41 individuals for D. virginiana. The estimated mean genetic diversity was high for both D. marsupialis (H e  = 0.77–0.78) and D. virginiana (H e  = 0.79–0.82). The survival of both species over time could be expected to increase if a metapopulation dynamics is favored over the coming decades, despite a 1.3% loss rate of forest cover. The monitoring of population size and genetic diversity is highly recommended to validate the trends suggested by the model; this is especially true for D. marsupialis, a species associated with conserved areas that are becoming progressively less abundant. This research provides information on the responses of common mammalian species to environmental changes such as deforestation.

The influence of breeding phenology on the genetic structure of four pond-breeding salamanders

Understanding metapopulation dynamics requires knowledge about local population dynamics and movement in both space and time. Most genetic metapopulation studies use one or two study species across the same landscape to infer population dynamics; however, using multiple co-occurring species allows for testing of hypotheses related to different life history strategies. We used genetic data to study dispersal, as measured by gene flow, in three ambystomatid salamanders (Ambystoma annulatum, A. maculatum, and A. opacum) and the Central Newt (Notophthalmus viridescens louisianensis) on the same landscape in Missouri, USA. While all four salamander species are forest dependent organisms that require fishless ponds to reproduce, they differ in breeding phenology and spatial distribution on the landscape. We use these differences in life history and distribution to address the following questions: (1) Are there species-level differences in the observed patterns of genetic diversity and genetic structure? and (2) Is dispersal influenced by landscape resistance? We detected two genetic clusters in A. annulatum and A. opacum on our landscape; both species breed in the fall and larvae overwinter in ponds. In contrast, no structure was evident in A. maculatum and N. v. louisianensis, species that breed during the spring. Tests for isolation by distance were significant for the three ambystomatids but not for N. v. louisianensis. Landscape resistance also contributed to genetic differentiation for all four species. Our results suggest species-level differences in dispersal ability and breeding phenology are driving observed patterns of genetic differentiation. From an evolutionary standpoint, the observed differences in dispersal distances and genetic structure between fall breeding and spring breeding species may be a result of the trade-off between larval period length and size at metamorphosis which in turn may influence the long-term viability of the metapopulation. Thus, it is important to consider life history differences among closely related and ecologically similar species when making management decisions.

The effects of sunfish on spotted salamander oviposition, hatching time, and larval survival

Introduced species have negative effects on amphibian populations by reducing local recruitment and consuming larvae before metamorphosis. Fish can naturally colonize ponds periodically because of flooding and connectivity with river floodplains. However, many fish introductions have been intentional for commercial, recreational, and biocontrol purposes. In southeast Missouri (USA), Ambystoma maculatum will attempt to breed in ponds even if introduced fish (Lepomis spp.) are present. We predicted that fish would have negative effects on salamander oviposition, hatching success and timing, and larval survival. In order to evaluate the effects of introduced fish on A. maculatum across life stages, we conducted pond surveys and a series of mesocosm experiments. Using field surveys, A. maculatum deposited significantly fewer eggs in ponds with fish. In short-term mesocosm experiments, we found that hatching time was not significantly affected by deposition site or fish cues, however, hatching success was lower for eggs deposited in fish ponds. No A. maculatum larvae survived when fish were present, regardless of egg deposition site. Our study is important because we found that, unless a female avoids depositing eggs with fish, one fish species can have profound effects on larval amphibian persistence. Therefore, small-scale fish introductions for recreation can act as a potential source for reduced recruitment and an increased risk of local extinction.

Decline in territory size and fecundity as a response to carrying capacity in an endangered songbird

Density-dependent processes are fundamental mechanisms for the regulation of populations. Ecological theories differ in their predictions on whether increasing population density leads to individual adjustments of survival and reproductive output or to dominance and monopolization of resources. Here, we use a natural experiment to examine which factors limit population growth in the only remaining population of the endangered pale-headed brush finch (Atlapetes pallidiceps). For three distinct phases (a phase of population suppression, 2001-2002; expansion due to conservation management, 2003-2008; and equilibrium phase, 2009-2014), we estimated demographic parameters with an integrated population model using population size, the proportion of successfully breeding pairs and their productivity, territory size, and mark-recapture data of adult birds. A low proportion of successful breeders due to brood parasitism (0.42, 95% credible interval 0.26-0.59) limited population growth before 2003; subsequent culling of the brood parasite resulted in a two-fold increase of the proportion of successful breeders during the 'expansion phase'. When the population approached the carrying capacity of its habitat, territory size declined by more than 50% and fecundity declined from 1.9 (1.54-2.27) to 1.3 (1.12-1.53) chicks per breeding pair, but the proportion of successful breeders remained constant (expansion phase: 0.85; 0.76-0.93; equilibrium phase: 0.86; 0.79-0.92). This study demonstrates that limiting resources can lead to individual adjustments instead of despotic behavior, and the individual reduction of reproductive output at high population densities is consistent with the slow life-history of many tropical species.

Lack of diversity at innate immunity Toll-like receptor genes in the Critically Endangered White-winged Flufftail (Sarothrura ayresi)

The White-winged Flufftail (Sarothrura ayresi) population is listed as globally Critically Endangered. White-winged Flufftails are only known to occur, with any regularity, in the high-altitude wetlands of South Africa and Ethiopia. Threats to the species include the limited number of suitable breeding sites in Ethiopia and severe habitat degradation and loss both in Ethiopia and South Africa. Toll-like receptors (TLRs) are increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune regions of the White-winged Flufftail similar to that observed in other bird species that have undergone population bottlenecks. Low TLR diversity in White-winged Flufftail indicates that this species is more likely to be threatened by changes to the environment that would potentially expose the species to new diseases. Thus, conservation efforts should be directed towards maintaining pristine habitat for White-winged Flufftail in its current distribution range. To date, no studies on immunogenetic variation in White-winged Flufftail have been conducted and to our knowledge, this is the first study of TLR genetic diversity in a critically endangered species.

Genetic assessment of captive red panda (Ailurus fulgens) population

Red panda (Ailurus fulgens) is threatened across its range by detrimental human activities and rapid habitat changes necessitating captive breeding programs in various zoos globally to save this flagship species from extinction. One of the ultimate aims of ex situ conservation is reintroduction of endangered animals into their natural habitats while maintaining 90 % of the founder genetic diversity. Advances in molecular genetics and microsatellite genotyping techniques make it possible to accurately estimate genetic diversity of captive animals of unknown ancestry. Here we assess genetic diversity of the red panda population in Padmaja Naidu Himalayan Zoological Park, Darjeeling, which plays a pivotal role in ex situ conservation of red panda in India. We generated microsatellite genotypes of fifteen red pandas with a set of fourteen loci. This population is genetically diverse with 68 % observed heterozygosity (H_O) and mean inbreeding (F_IS) coefficient of 0.05. However population viability analysis reveals that this population has a very low survival probability (<2 %) and will rapidly loose its genetic diversity to 37 % mainly due to small population size and skewed male-biased sex ratio. Regular supplementation with a pair of adult individuals every five years will increase survival probability and genetic diversity to 99 and 61 % respectively and will also support future harvesting of individuals for reintroduction into the wild and exchange with other zoos.

Movement ecology of amphibians: from individual migratory behaviour to spatially structured populations in heterogeneous landscapes,

Both genetic cohesion among local populations of animals and range expansion depend on the frequency of dispersers moving at an interpatch scale. Animal movement has an individual component that reflects behaviour and an ecological component that reflects the spatial organization of populations. The total movement capacity of an individual describes maximum movement distance theoretically achievable during a lifetime, whereas its variation among the members of a local population determines the magnitude of interpatch movements and thus of gene flow between neighbouring patches within metapopulation or patchy population systems. Here, I review information on dispersal and migration as components of the movement capacity of juvenile and adult pond-breeding amphibians and discuss how these components inform the spatial structure of populations. Amphibians disperse as juveniles and adults, but movement distances detected in tracking or capture–mark–recapture studies are usually far below the corresponding estimates based on molecular gene-flow data. This discrepancy reflects the constraints of available tracking methods for free-ranging individuals leading to inappropriate surrogates of annual movement capacity, but can be resolved using probabilistic approaches based on dispersal functions. There is remarkable capacity for and plasticity in movements in amphibians. Annual within-patch movements (migrations) of individuals can be large and likely represent an underestimated capacity for movement at the interpatch scale. Landscape resistance may influence the paths of dispersing amphibians, but rarely impedes interpatch movements. Juveniles emigrating unpredictably far from the natal pond and adults switching from within-patch migrations to dispersal to another patch demonstrate the plasticity of individual movement behaviour. Three basic conclusions can be drawn with respect to the linkage of individual movement behaviour and spatial or genetic structure of local amphibian populations embedded in a heterogeneous landscape: (1) individual movements or consecutive short-term series of movements are misleading surrogate measures of total movement capacity; (2) probabilistic modelling of movement capacity is the best available behavioural predictor of interpatch gene flow; (3) connectivity of local populations in heterogeneous landscapes is less affected by landscape resistance than previously expected.

Drought, deluge and declines: the impact of precipitation extremes on amphibians in a changing climate

The Class Amphibia is one of the most severely impacted taxa in an on-going global biodiversity crisis. Because amphibian reproduction is tightly associated with the presence of water, climatic changes that affect water availability pose a particularly menacing threat to both aquatic and terrestrial-breeding amphibians. We explore the impacts that one facet of climate change—that of extreme variation in precipitation—may have on amphibians. This variation is manifested principally as increases in the incidence and severity of both drought and major storm events. We stress the need to consider not only total precipitation amounts but also the pattern and timing of rainfall events. Such rainfall “pulses” are likely to become increasingly more influential on amphibians, especially in relation to seasonal reproduction. Changes in reproductive phenology can strongly influence the outcome of competitive and predatory interactions, thus potentially altering community dynamics in assemblages of co-existing species. We present a conceptual model to illustrate possible landscape and metapopulation consequences of alternative climate change scenarios for pond-breeding amphibians, using the Mole Salamander, Ambystoma talpoideum, as an example. Although amphibians have evolved a variety of life history strategies that enable them to cope with environmental uncertainty, it is unclear whether adaptations can keep pace with the escalating rate of climate change. Climate change, especially in combination with other stressors, is a daunting challenge for the persistence of amphibians and, thus, the conservation of global biodiversity.