Past bottlenecks and current population fragmentation of endangered huemul deer (Hippocamelus bisulcus): implications for preservation of genetic diversity

Genetic diversity in ex situ populations of the endangered Leontopithecus chrysomelas and implications for its conservation

Leontopithecus chrysomelas, the Golden-headed Lion Tamarin (GHLT), is an endangered and endemic Neotropical primate from the Atlantic Forest of Brazil that has suffered a reduction of its habitat and population size in the wild. Ex situ populations have been established as a relevant alternative to safeguard the species and retain its genetic diversity and evolutionary potential. This study evaluated the genetic diversity and structure of the two main Brazilian captive populations of GHLT, which have been under human care at the Primatology Center of Rio de Janeiro (CPRJ) and the Zoological Park Foundation of São Paulo (FPZSP). Our results revealed levels of genetic diversity overall comparable to those observed for other Leontopithecus species and for ex situ and in situ populations of GHLT previously studied. Bayesian and principal coordinate analyses showed a moderate differentiation between CPRJ and FPZSP populations. Both populations presented observed heterozygosity values higher than expected heterozygosity values for most of the microsatellites used in this study, suggesting that the management has been efficient in avoiding an increase in homozygosity. However, simulations point to a significant loss of genetic diversity in the next 100 years, mainly in the FPZSP population. Such data are relevant for further decision-making on the metapopulation management of L. chrysomelas in captive conditions and for integrating in situ and ex situ conservation plans.

Low STR variability in the threatened marsh deer, Blastocerus dichotomus, detected through amplicon sequencing in non-invasive samples

Blastocerus dichotomus is the largest deer in South America. We have used 25 microsatellite markers detected and genotyped by Next Generation Sequencing to estimate the genetic variability of B. dichotomus in Argentina, where most of its populations are threatened. Primer design was based on the sequence of a shallow partial genome (15,967,456 reads; 16.66% genome coverage, mean depth 1.64) of a single individual. From the thousands of microsatellite loci found, even under high stringency selection, we chose and tested a set of 80 markers on 30 DNA samples extracted from tissue and feces from three Argentinean populations. Heterozygosity levels were low across all loci in all populations (H=0.31 to 0.40). Amplicon sequencing is a fast, easy, and affordable technique that can be very useful for the characterization of microsatellite marker sets for the conservation genetics of non-model organisms. This work is also one of the first ones to use amplicon sequencing in non-invasive samples and represents an important development for the study of threatened species.

Multi-taxon biodiversity assessment of Southern Patagonia: Supporting conservation strategies at different landscapes

In the last years, different spatial analyses were developed to support multi-taxon biodiversity conservation strategies. In fact, the use of species distribution models as input allowed to create spatial decision-support maps. Of special interest are maps of potential biodiversity (MPB), which define distribution and ecological requirements of relevant species and maps of priority conservation areas (MPCA), which define priority areas considering endemism and richness. The objective of this paper was to assess multi-taxon biodiversity based on two different spatial analyses and to test their efficiency to support conservation decision at Patagonia. We computed 119 potential habitat suitability maps (one deer, birds, lizards, darkling-beetles, plants) with ENFA (Environmental Niche Factor Analysis) and 15 environmental variables, using Biomapper software. ENFA calculate two ecological indexes (marginality and specialization) which describe the narrowness of species niches and how extreme are the optimum environmental conditions related to the whole study area. These maps were combined obtaining a MPB and MPCA using Zonation software. Multivariate analyses were performed to compare methodologies, analysing environmental variables, ecological areas, forest types and protected areas. Multivariate and ecological indexes showed that deer, lizards and darkling-beetles presented a narrow range, while birds and plants presented a large range of marginality and specialization mainly related to vegetation and climate. At provincial level, highest potential biodiversity and conservation priority values were related to shrublands and humid steppes. However, MPCA showed higher values related to forests and alpine vegetation due to endemism, while MPB showed differences among forest types. These analyses showed that the most valuable areas were not represented in the protected areas, however, many higher conservation priority values were found inside the protected compared with unprotected areas. Different spatial decision-support maps presented similar outputs at provincial scale, but differed in the forest landscape matrix. Both methodologies can be used to plan conservation strategies depending on the specific objectives (e.g. highlighting richness or endemism).

Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations

Abstract Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.

Extinction risk assessment of a Patagonian ungulate using population dynamics models under climate change scenarios

Climate change affects population cycles of several species, threatening biodiversity. However, there are few long-term studies on species with conservation issues and restricted distributions. Huemul is a deer endemic to the southern Andes in South America and it is considered endangered mostly due to a 50% reduction of its distribution over the last 500 years. To assess environmental variables potentially affecting huemul population viability and the impact of climate change, we developed population dynamics models. We used a 14-year survey data from Bernardo O'Higgins National Park, coastal Chilean Patagonia. We used Ricker models considering winter and spring temperatures and precipitation as variables influencing huemul population dynamics. We used the Bayesian information criterion (BIC) to select models with the greatest predictive power. The two best models (ΔBIC < 2) included winter temperature and density-dependence population growth drivers. The best model considered a lateral effect, where winter temperature influences carrying capacity and the second best a vertical effect with winter temperature influencing R_max and carrying capacity. Population viability was evaluated using those models, projecting them over a 100-year period: (a) under current conditions and (b) under conditions estimated by Global Climate Models for 2050 and 2070. The extinction risk and quasi-extinction were estimated for this population considering two critical huemul abundance levels (15 and 30 individuals) for persistence. The population is currently in a quasi-extinction process, with extinction probabilities increasing with climate change. These results are crucial for conservation of species like huemul that have low densities and are threatened by climate change.

Sarcocystis spp. infection in South American deer huemul (Hippocamelus bisulcus) and pudu (Pudu puda) from Patagonian National Parks, Argentina

Sarcocystis spp. are intracellular protozoan parasites with heteroxenous life cycles. This study described Sarcocystis spp. infection in adult South American native deer huemul (Hippocamelus bisulcus) and pudu (Pudu puda). Heart, diaphragm, tongue, and skeletal muscle samples were collected from 5 huemuls and 2 pudus, found dead in National Parks. Direct microscopic examination, transmission electron microscopy, PCR, and sequencing were performed. Sarcocystis spp. microscopic thin-walled cysts were identified in 3 huemuls and 1 pudu. Several cysts from 1 huemul and 1 pudu were observed by TEM; ultrastructure was similar to previously reported as cyst wall type 17 and types 2 and 8, respectively. Fragments of the 18S rRNA and cytochrome c oxidase subunit I (cox1) genes were amplified and sequenced from 3 individual cysts from 2 huemuls and 2 cysts from the pudu. The sequences from huemuls showed a high identity among them (> 99%) at both amplified targets. The highest identities were > 99.7% at 18S rRNA and 93% at cox1 with S. tarandivulpes sequences. The 18S rRNA gene sequences from pudus showed an identity > 99.7% with Sarcocystis sp., S. taeniata, and S. linearis sequences, while the cox1 sequences were different, one showing 99.42% identity with S. venatoria and the other 98.22% with S. linearis. A single species, similar to S. tarandivulpes, was identified in all huemul samples while 2 molecularly different Sarcocystis spp. were found in 1 pudu with high similarities to either S. venatoria or to S. linearis, S. taeniata-like, and S. morae. Based on the cox1 sequence identities, at least the Sarcocystis sp. in huemuls might represent a new species, primarily occurring in this host. Additional sarcocyst isolates from both hosts need to be examined molecularly in order to firmly establish whether these species are indeed native to huemuls and/or pudus or are derived from introduced deer species.

Already at the bottom? Demographic declines are unlikely further to undermine genetic diversity of a large Arctic ungulate: muskox, Ovibos moschatus (Artiodactyla: Bovidae)

Low genetic diversity is associated with low fitness and evolutionary potential, yet the demographic and life-history traits of some species contribute to low genetic diversity, without empirical evidence of negative impacts on fitness. Modelling past and future trajectories of genetic diversity under different demographic scenarios can provide insight into how genetic variation might impact population fitness. The muskox is an Arctic species that has undergone multiple population bottlenecks and, although populations have rebounded repeatedly, two large populations have recently declined by &gt; 50%. It is unclear how these demographic patterns influence muskox genetic diversity and fitness. We compared the genetic diversity of Canadian muskox populations undergoing opposing population trends. Genotyping 84 mainland and 244 Victoria Island individuals at ten microsatellite loci revealed low genetic variation (Victoria Island, mean allelic richness 1.66, expected heterozygosity 0.16; mainland, mean allelic richness 2.58, expected heterozygosity 0.41), with no evidence of further reductions in diversity subsequent to recent demographic declines. Bayesian modelling showed that a 1900s bottleneck contributed to the lack of diversity in contemporary populations, and forward-in-time simulations suggested little effect on genetic diversity over the next 100 years. Muskoxen might have reached a genetic diversity minimum, and additional research will be needed to determine their capacity to adapt to rapid changes in selective pressures in a rapidly changing Arctic.

Protected areas' effectiveness under climate change: a latitudinal distribution projection of an endangered mountain ungulate along the Andes Range

BACKGROUND

Climate change is one of the greatest threats to biodiversity, pushing species to shift their distribution ranges and making existing protected areas inadequate. Estimating species distribution and potential modifications under climate change are then necessary for adjusting conservation and management plans; this is especially true for endangered species. An example of this issue is the huemul (Hippocamelus bisulcus), an endemic endangered deer from the southern Andes Range, with less than 2,000 individuals. It is distributed in fragmented populations along a 2,000 km latitudinal gradient, in Chile and Argentina. Several threats have reduced its distribution to <50% of its former range.

METHODS

To estimate its potential distribution and protected areas effectiveness, we constructed a species distribution model using 2,813 huemul presence points throughout its whole distribution range, together with 19 bioclimatic layers and altitude information from Worldclim. Its current distribution was projected for years 2050 and 2070 using five different Global Climate Models estimated for scenarios representing two carbon Representative Concentration Routes (RCP)-RCP4.5 and RCP6.0.

RESULTS

Based on current huemul habitat variables, we estimated 91,617 km2 of suitable habitat. In future scenarios of climate change, there was a loss of suitable habitat due to altitudinal and latitudinal variation. Future projections showed a decrease of 59.86-60.26% for the year 2050 and 58.57-64.34% for the year 2070 according to RCP4.5 and RCP6.0, respectively. Protected areas only covered only 36.18% of the present distribution, 38.57-34.94% for the year 2050 and 30.79-31.94% for 2070 under climate change scenarios.

DISCUSSION

Modeling current and future huemul distributions should allow the establishment of priority conservation areas in which to focus efforts and funds, especially areas without official protection. In this way, we can improve management in areas heavily affected by climate change to help ensure the persistence of this deer and other species under similar circumstances worldwide.

Predicting the potential distribution of the Endangered huemul deer Hippocamelus bisulcus in North Patagonia

Habitat loss is one of the main threats to wildlife, particularly large mammals. Estimating the potential distribution of threatened species to guide surveys and conservation is crucial, primarily because such species tend to exist in small fragmented populations. The Endangered huemul deer Hippocamelus bisulcus is endemic to the southern Andes of Chile and Argentina. Although the species occurs in the Valdivian Ecoregion, a hotspot for biodiversity, we have no information on its occupancy and potential distribution in this region. We built and compared species distribution models for huemul using the maximum entropy approach, using 258 presence records and sets of bioclimatic and geographical variables as predictors, with the objective of assessing the potential distribution of the species in the Valdivian Ecoregion. Annual temperature range and summer precipitation were the predictive variables with the greatest influence in the best-fitting model. Approximately 12,360 km2 of the study area was identified as suitable habitat for the huemul, of which 30% is included in the national protected area systems of Chile and Argentina. The map of potential distribution produced by our model will facilitate prioritization of future survey efforts in other remote and unexplored areas in which huemul have not been recorded since the 1980s but where there is a high probability of their occurrence.

Blood mineral concentrations in the endangered huemul deer (Hippocamelus bisulcus) from Chilean Patagonia

Concentrations of calcium, magnesium, copper, zinc, and selenium were measured in plasma from 11 huemul (Hippocamelus bisulcus) from Chilean Patagonia. Except for zinc and copper, concentrations of these minerals were similar to those of other deer species.

Effective population size, genetic variation, and their relevance for conservation: the bighorn sheep in Tiburon Island and comparisons with managed artiodactyls

The amount of genetic diversity in a finite biological population mostly depends on the interactions among evolutionary forces and the effective population size (N(e)) as well as the time since population establishment. Because the N(e) estimation helps to explore population demographic history, and allows one to predict the behavior of genetic diversity through time, N(e) is a key parameter for the genetic management of small and isolated populations. Here, we explored an N(e)-based approach using a bighorn sheep population on Tiburon Island, Mexico (TI) as a model. We estimated the current (N(crnt)) and ancestral stable (N(stbl)) inbreeding effective population sizes as well as summary statistics to assess genetic diversity and the demographic scenarios that could explain such diversity. Then, we evaluated the feasibility of using TI as a source population for reintroduction programs. We also included data from other bighorn sheep and artiodactyl populations in the analysis to compare their inbreeding effective size estimates. The TI population showed high levels of genetic diversity with respect to other managed populations. However, our analysis suggested that TI has been under a genetic bottleneck, indicating that using individuals from this population as the only source for reintroduction could lead to a severe genetic diversity reduction. Analyses of the published data did not show a strict correlation between H(E) and N(crnt) estimates. Moreover, we detected that ancient anthropogenic and climatic pressures affected all studied populations. We conclude that the estimation of N(crnt) and N(stbl) are informative genetic diversity estimators and should be used in addition to summary statistics for conservation and population management planning.

Huemul heresies: beliefs in search of supporting data. 2. Biological and ecological considerations

Scarce information from remnant huemul (Hippocamelus bisulcus) populations in marginal habitats can lead to erroneous interpretations of the species’ natural history, such as assumptions of being a highly inflexible species. We evaluated discrepancies between historical accounts and recent interpretations regarding biological and ecological traits to better understand factors preventing recovery of highly endangered huemul. Early information supports the theory that huemul are currently living under suboptimal conditions. We find variability to be the norm for huemul, as with other cervids, in regard to antler characteristics, group size and density, sexual segregation, and social and feeding behaviours. No evidence supports competition and disease from livestock or red deer as having caused declines or preventing recovery. Instead, livestock management, particularly presence of people and dogs, creates incompatibilities. Where red deer are sympatric with huemul, red deer are outnumbered by livestock by 2100%, and being regularly inspected at slaughter, livestock provide a good proxy for diseases afflicting red deer. Inadequate antipredator responses due to evolutionary absence of cursorial predators are unsupported as several Canis species coexisted with huemul, overlapping with dogs that arrived with Paleoindians. Three populations have increased despite high predator density. Age at maturity for huemul is 1 year, with evidence that fawns may also breed. Reported twinning needs confirmation, but occurs in congeneric taruca (H. antisensis) and other Odocoilines, and huemul frequently raise fawns successfully every year; life cycle calculations should apply these parameters. Like taruca, dominance group breeding systems have been described repeatedly. Although huemul bucks were recently claimed unique by displaying territoriality year-round, data do not support such behaviour. Two sole dispersal records (8 and 15.5 km) are unlikely to represent maximum dispersal capacity and do not support barriers assumed from few kilometres of unsuitable habitat. Huemul using 500 ha could predictably disperse up to 90 km, well within the ranges of other cervids. Mistakenly assuming barriers and underestimating reproductive capacity may distract from discovering the factors affecting recolonisations. Sustained recovery may depend on re-establishing source populations on more productive habitats, guided by zooarcheological and historical data.