The distribution and conservation status of Tapirus terrestris in the South American Atlantic Forest

Tapirus terrestris is the largest South American land mammal, with an extensive historical distribution and capable of occupying diverse habitats, and yet its populations have declined across its range. In order to provide baseline data on the conservation status of tapirs in the Atlantic Forest, we conducted a long-term study in one landscape, visited 93 forests, and received 217 expert reports over the 15-year study. We estimate that 2,665–15,992 tapirs remain in 48 confirmed populations, occupying 26,654 km2 of forest or 1.78% of its original range in the biome. Historically, hunting and deforestation were the main causes of decline, but today population isolation is the principal long-term threat. Vortex models indicate that 31.3–68.8% and 70.8–93.8% of the populations are demographically and genetically non-viable over the next 100 years, respectively, and that only 3–14 populations are viable when considering both variables. Habitat use data indicate that tapirs are adaptable to disturbed and secondary forests and will use diverse tree plantations and agricultural lands but hunting and highways keep populations isolated. Reserve staff report tapirs as common/abundant at 62.2% of the sites, and populations as stable and growing in 60% and 36% of the sites, respectively, and there is ample habitat in the biome for a population expansion, but overcoming the causes of isolation will be necessary for this to occur. Lack of adequate funding for protecting reserves is a chronic threat throughout the biome, especially in federal and state/provincial reserves, and increased funding will be necessary to implement effective conservation plans.

Modelling Multi-Species Connectivity at the Kafue-Zambezi Interface: Implications for Transboundary Carnivore Conservation

Linking wildlife areas with corridors facilitating species dispersal between core habitats is a key intervention to reduce the deleterious effects of population isolation. Large heterogeneous networks of areas managed for wildlife protection present site- and species-scale complexity underpinning the scope and performance of proposed corridors. In Southern Africa, the Kavango-Zambezi Transfrontier Conservation Area seeks to link Kafue National Park to a cluster of wildlife areas centered in Namibia and Botswana. To assess and identify potential linkages on the Zambian side, we generated a high-resolution land cover map and combined empirical occurrence data for Lions (Panthera leo), Leopards (Panthera pardus) and Spotted Hyena (Crocuta crocuta) to build habitat suitability maps. We then developed four connectivity models to map potential single and multi-species corridors between Kafue and the Zambezi River border with Namibia. Single and multi-species connectivity models selected corridors follow broadly similar pathways narrowing significantly in central-southern areas of the Kafue-Zambezi interface, indicating a potential connectivity bottleneck. Capturing the full extent of human disturbance and barriers to connectivity remains challenging, suggesting increased risk to corridor integrity than modelled here. Notwithstanding model limitations, these data provide important results for land use planners at the Kafue-Zambezi Interface, removing much speculations from existing connectivity narratives. Failure to control human disturbance and secure corridors will leave Kafue National Park, Zambia’s majority component in the Kavango-Zambezi Transfrontier Conservation Area, isolated.

Estimating the number of COVID-19 cases from population isolation level

We use the logistic function to estimate the number of individuals infected by a virus in a period of time as a function of social isolation level in the previous period of the infection occurrences. Each period is composed by a fixed date range in days which the social isolation is supposed to take effect over the virus spread in the next date range. The sample is the COVID-19 cases and social isolation level data from São Paulo State, Brazil. The proposed method is divided into two stages: 1) The logistic function is fitted against COVID-19 empirical data to obtain the function parameters; 2) the function parameters, except for the overall growth rate, and the mean of social isolation level for all periods of time are used to calculate a constant. The logistic growth rate for each period of time is calculated using the constant and the isolation level for that period. The number of cases in a period is estimated using the logistic function and the growth rate from previous period of time to obtain the effect of social isolation during the elapsed time. The period of time that produces a better correlation between empirical and estimated data was 5 days. We conclude the method performs a data estimation with high correlation with the empirical data.

Identification and characterization of hPSC-derived FOXA2+ progenitor cells with ventricular cardiac differentiation potential

While much progress has been made in understanding early cardiac development, the precise mechanisms that specify the different cardiomyocyte subtypes remain poorly understood. Recent data from our lab have shown that transient Foxa2 expression identifies a progenitor population with exclusive ventricular differentiation potential in the mouse heart. Here we have translated this concept to the human pluripotent stem cell (hPSC) system. Using a FOXA2-GFP reporter cell line we characterized expression of FOXA2 during hPSC cardiac differentiation and found that a subset of cardiac mesoderm precursors transiently expresses FOXA2. Gene expression analysis of FOXA2+ and FOXA2- cardiac mesoderm revealed that both populations similarly express early cardiac specification markers such as PDGFRA, TBX5, and ISL1, while other key candidates including TBX20 and GATA4 are significantly upregulated in the FOXA2+ population. Isolation and subsequent differentiation of FOXA2+ and FOXA2- populations demonstrates their comparable differentiation potential to both cardiomyocytes and epicardial cells. However, cardiomyocytes derived from FOXA2+ precursors showed enhanced differentiation efficiency toward ventricular cardiomyocytes compared to cardiomyocytes derived from FOXA2- precursors. To identify new mechanisms that regulate ventricular specification, we performed small molecule screening and found that inhibition of the EGFR pathway strongly increased the cardiac mesoderm population in general, and the FOXA2+ precursors in particular. Finally, we have identified a combination of cell surface markers to specifically isolate FOXA2+ cardiac precursors. In summary, our results suggest that FOXA2+ cardiac mesoderm harbors ventricular-specific differentiation potential and isolation of these cells permits the generation of cultures enriched for ventricular cardiomyocytes. Generating such enriched cardiac populations will be relevant for regenerative medicine approaches, as well as for disease modeling from induced pluripotent stem cells.

Comparative population genetics of swimming crab host (Portunus pelagicus) and common symbiotic barnacle (Octolasmis angulata) in Vietnam

Background By comparing spatial geographical structures of host populations with that of their symbionts light can be shed on their biological interactions, and the degree of congruence between host and symbiont phylogeographies should reflect their life histories and especially dispersal mechanisms. Methods Here, we analyzed the genetic diversity and structure of a host, the blue swimming crab, Portunus pelagicus, and its symbiotic pedunculate barnacle Octolasmis angulata from six location sites representing three geographic regions (north, central and south) along the Vietnam coastline. High levels of congruence in their phylogeographic patterns were expected as they both undergo planktonic larval stages. Results Based on the COI mtDNA markers, O. angulata populations showed higher genetic diversity in comparison with their host P. pelagicus (number of haplotype/individuals, haplotype and nucleotide diversity are 119/192, 0.991 ± 0.002 and 0.02; and 89/160, 0.913 ± 0.02 and 0.015, respectively). Pairwise Fst and AMOVA analyses showed a more pronounced population structure in the symbiotic barnacle than in its crab host. The DAPC analyses identified three genetic clusters. However, both haplotype networks and scatter plots supported connectivity of the host and the symbiotic barnacle throughout their distribution range, except for low subdivision of southern population. Isolation by distance were detected only for the symbiont O. angulata (R2 = 0.332, P = 0.05), while dbMEM supported spatial structure of both partners, but only at MEM-1 (Obs. 0.2686, P < 0.01 and Obs. 0.2096, P < 0.01, respectively).

Lizards of a different stripe: phylogenetics of the Pedioplanis undata species complex (Squamata, Lacertidae), with the description of two new species

The lacertid genus Pedioplanis is a moderately speciose group of small-bodied, cryptically-colored lizards found in arid habitats throughout southern Africa. Previous phylogenetic work on Pedioplanis has determined its placement within the broader context of the Lacertidae, but interspecific relations within the genus remain unsettled, particularly within the P. undata species complex, a group largely endemic to Namibia. We greatly expanded taxon sampling for members of the P. undata complex and other Pedioplanis, and generated molecular sequence data from 1,937 bp of mtDNA (ND2 and cytb) and 2,015 bp of nDNA (KIF24, PRLR, RAG-1) which were combined with sequences from GenBank resulting in a final dataset of 455 individuals. Both maximum likelihood and Bayesian analyses recover similar phylogenetic results and reveal the polyphyly of P. undata and P. inornata as presently construed. We confirm that P. husabensis is sister to the group comprising the P. undata complex plus the Angolan sister species P. huntleyi + P. haackei and demonstrate that P. benguelensis lies outside of this clade in its entirety. The complex itself comprises six species including P. undata, P. inornata, P. rubens, P. gaerdesi and two previously undescribed entities. Based on divergence date estimates, the P. undata species complex began diversifying in the late Miocene (5.3 ± 1.6 MYA) with the most recent cladogenetic events dating to the Pliocene (2.6 ± 1.0 MYA), making this assemblage relatively young compared to the genus Pedioplanis as a whole, the origin of which dates back to the mid-Miocene (13.5 ± 1.8 MYA). Using an integrative approach, we here describe Pedioplanis branchisp. nov. and Pedioplanis mayerisp. nov. representing northern populations previously assigned to P. inornata and P. undata, respectively. These entities were first flagged as possible new species by Berger-Dell’mour and Mayer over thirty years ago but were never formally described. The new species are supported chiefly by differences in coloration and by unique amino acid substitutions. We provide comprehensive maps depicting historical records based on museum specimens plus new records from this study for all members of the P. undata complex and P. husabensis. We suggest that climatic oscillations of the Upper Miocene and Pliocene-Pleistocene era in concert with the formation of biogeographic barriers have led to population isolation, gene flow restrictions and ultimately cladogenesis in the P. undata complex.

Genetic Consequences of Fence Confinement in a Population of White-Tailed Deer

Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 white-tailed deer confined within a 1184 ha fence to quantify changes in genetic diversity and inbreeding over the first 12 years of confinement. Genetic diversity was sustained over the course of the study, remaining comparable to unconfined white-tailed deer populations. Uneroded genetic diversity suggests that genetic drift is mitigated by a low level of gene flow, which supports field observations that the fence is not completely impermeable. In year 9 of the study, we observed an unexpected influx of mtDNA diversity and drop in inbreeding as measured by FIS. A male harvest restriction imposed that year increased male survival, and more diverse mating may have contributed to the inbreeding reduction and temporary genetic diversity boost we observed. These data add to our understanding of the long-term impacts of fences on wildlife, but also highlight the importance of continued monitoring of confined populations.

When ecological marginality is not geographically peripheral: exploring genetic predictions of the centre-periphery hypothesis in the endemic plantLilium pomponium

BackgroundQuantifying variation of genetic traits over the geographical range of species is crucial for understanding the factors driving their range dynamics. The center-periphery hypothesis postulates, and many studies support, the idea that genetic diversity decreases and genetic differentiation increases toward the geographical periphery due to population isolation. The effects of environmental marginality on genetic variation has however received much less attention.MethodsWe tested the concordance between geographical and environmental gradients and the genetic predictions of center-periphery hypothesis for endemicLilium pomponiumin the southern Alps.ResultsWe found little evidence for concordance between genetic variation and both geographical and environmental gradients. Although the prediction of increased differentiation at range limits is met, genetic diversity does not decrease towards the geographical periphery. Increased differentiation among peripheral populations, that are not ecologically marginal, may be explained by a decrease in habitat availability that reduces population connectivity. In contrast, a decrease of genetic diversity along environmental but not geographical gradients may be due to the presence of low quality habitats in the different parts of the range of a species that reduce effective population size or increase environmental constraints. As a result, environmental factors may affect population dynamics irrespective of distance from the geographical center of the range. In such situations of discordance between geographical and environmental gradients, the predictions of decreasing genetic diversity and increasing differentiation toward the geographical periphery may not be respected.

Recent genetic connectivity and clinal variation in chimpanzees

Much like humans, chimpanzees occupy diverse habitats and exhibit extensive behavioural variability. However, chimpanzees are recognized as a discontinuous species, with four subspecies separated by historical geographic barriers. Nevertheless, their range-wide degree of genetic connectivity remains poorly resolved, mainly due to sampling limitations. By analyzing a geographically comprehensive sample set amplified at microsatellite markers that inform recent population history, we found that isolation by distance explains most of the range-wide genetic structure of chimpanzees. Furthermore, we did not identify spatial discontinuities corresponding with the recognized subspecies, suggesting that some of the subspecies-delineating geographic barriers were recently permeable to gene flow. Substantial range-wide genetic connectivity is consistent with the hypothesis that behavioural flexibility is a salient driver of chimpanzee responses to changing environmental conditions. Finally, our observation of strong local differentiation associated with recent anthropogenic pressures portends future loss of critical genetic diversity if habitat fragmentation and population isolation continue unabated.