The coming of age of conservation genetics in Latin America: what has been achieved and what needs to be done

Understanding the conservation-genetics gap in Latin America: challenges and opportunities to integrate genetics into conservation practices

Introduction: Integrating genetic data into conservation management decisions is a challenging task that requires strong partnerships between researchers and managers. Conservation in Latin America is of crucial relevance worldwide given the high biodiversity levels and the presence of hotspots in this region. Methods: We conducted a survey across Latin America to identify gaps and opportunities between genetic researchers and conservation managers. We aimed to better understand conservation managers' points of view and how genetic research could help conservation practitioners to achieve their goals, by implementing genetic assessments that could effectively inform conservation practices. We distributed an online survey via four regional collaborating organizations and 32 focal points based in 20 Latin American countries. The target respondents were conservation managers of species or areas in Latin America. Results: We collected a total of 468 answered questionnaires from 21 Latin American countries. Most respondents (44%) were from an academic or research institution while non-academics were mainly from non-governmental institutions (30%) and government agencies (25%). Most respondents (65%) have performed or used genetic assessments in their managed area or species, either alone, in partnership, contracting someone else or using published results. For the majority of this group, the genetic results were relevant to their conservation management goals, helping to inform management decisions. Respondents that had not performed genetic assessments (35%) were mainly from the non-academic group, and their main barriers were limited access to funds, genetic lab facilities, and trained personnel to design studies and conduct lab work. Discussion: From the findings, we describe the current situation and provide a general diagnosis of the conservation-genetics gap in Latin America. We describe the gender gap, academic-practitioner co-development of conservation questions and projects, and the nationality and residency of Latin American conservation managers in relation to the countries where they work. We discuss opportunities to co-create research questions and co-develop studies based on conservation practitioners' needs. We offer recommendations for overcoming barriers to integrate genetic information into conservation actions, and advance agendas that fit the needs and realities of the highly heterogeneous, biodiverse and challenging Latin American region.

Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.

Genetic divergence and demography of pudu deer (Pudu puda) in five provinces of southern Chile, analyzed through latitudinal and longitudinal ranges

Pudu deer (Pudu puda) is endemic to the temperate rainforests of Chile. Genetic studies at different geographic scales for this species are required to better determine the genetic divergence within and among populations and their demography across the distribution range. These data can provide unique insights into the species or population status for conservation plans and decision-makers. We analyzed the mtDNA control region (CR) and cytochrome b (Cyt b) sequences of pudu deer in five provinces of southern Chile located at different latitudinal locations (Cautín, Valdivia, Osorno, Llanquihue and Chiloé Island) and three geographic areas within the studied provinces, representative of different longitudinal sites (Andes range, Central Valley and Coastal Range), to understand their genetic divergence and demography. The haplotype (H) and nucleotide (Π) diversities of CR and Cyt b ranged from 0.64286 to 0.98333 and from 0.00575 to 0.01022, respectively. CR diversity was significantly different among provinces, with Valdivia showing higher values than Llanquihue and Chiloé Island (H = 0.98333 vs. 0.64286–0.92727, P < 0.05). Cyt b variation also showed significant differences among provinces, particularly, among Cautín and Llanquihue (H = 1.000 vs. 0.222, P < 0.05). Genetic structuring among provinces was relatively high, as indicated by the FST index (FST = 0.41905). Clustering analysis indicated the presence of a distinctive cluster for Chiloé Island individuals. Fu’s FS and Tajima’s D based on CR revealed significant, negative deviations from equilibrium for Chiloé Island (D = -1.65898), Valdivia (Fs = -7.75335) and Llanquihue (Fs = -3.93267), suggesting population expansion in these provinces. Analysis at the longitudinal range showed significant differences among areas based on Π (P < 0.05), with the Andes range and Central Valley showing higher diversity than the Coastal Range. Neither population structuring (FST = 0.01360, P > 0.05) nor distinctive clusters in the longitudinal range were observed. Fu’s Fs and Tajima’s D were negative and significant for the Coastal Range based on CR (Fs = -6.64752, P < 0.001) and Cyt b (D = -1.74110, P < 0.05), suggesting the existence of population expansion. Our results suggest that pudu deer in the analyzed provinces is a genetically structured species, which could be associated with reduced panmixia among populations. The genetic divergence pattern and the population expansion recorded are likely to be associated with past processes of recolonization after Pleistocene glaciation events.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

Use of genetic tools to assess predation on reintroduced howler monkeys (Alouatta caraya) in Northeastern Argentina

Despite strong support from the media, the reintroduction of animals into natural environments does not always achieve its goal. Alouatta caraya is the primate species facing the greatest hunting pressure due to the illegal pet trade in Argentina. Confiscations of this species are common, as is the voluntary surrender of animals by owners no longer able or willing to care for them. These animals ultimately arrive at rehabilitation centers and, in many cases, are released into natural environments that may differ from the original sites where they were captured. Until recently, the lack of genetic analysis of the individuals involved led to biased relocation decisions. We followed the reintroduction of 12 A. caraya individuals in a protected area (Isla Palacio, Misiones, Argentina). The presence of potential predators such as pumas (Puma concolor) and jaguars (Panthera onca) in this area was confirmed by camera traps, footprints and feces. After the disappearance of four A. caraya at the reintroduction site, we investigated the applicability of genetic assignment tests based on genotypic data to accurately identify predated individuals. Genetic analyses allowed us to determine the predator species (P. onca) and to identify the predated individuals as two of the reintroduced animals. This procedure is promising for identifying the remains of predated individuals, and can contribute to the design of reintroduction policies based on scientific evidence.

Genetic assignment of illegally trafficked neotropical primates and implications for reintroduction programs

The black and gold howler monkey (Alouatta caraya) is a neotropical primate threatened by habitat loss and capture for illegal trade in Argentina. Using multilocus microsatellite genotypes from 178 A. caraya individuals sampled from 15 localities in Argentina, we built a genotype reference database (GRDB). Bayesian assignment methods applied to the GRDB allowed us to correctly re-assign 73% of individuals to their true location of origin and 93.3% to their cluster of origin. We used the GRDB to assign 22 confiscated individuals (17 of which were reintroduced), and 3 corpses to both localities and clusters of origin. We assigned with a probability >70% the locality of origin of 14 individuals and the cluster of origin of 21. We found that most of the confiscated individuals were assigned to one cluster (F-Ch-C) and two localities included in the GRDB, suggesting that trafficked A. caraya primarily originated in this area. Our results reveal that only 4 of 17 reintroduced individuals were released in sites corresponding to their cluster of origin. Our findings illustrate the applicability of genotype databases for inferring hotspots of illegal capture and for guiding future reintroduction efforts, both of which are essential elements of species protection and recovery programs.

Molecular genetic studies of Chilean avifauna: an overview about current progress

The biodiversity of Chilean avifauna has been shaped by geological events, geographical factors and extreme climatic regimens. Molecular genetic studies developed to date have begun to provide valuable information to elucidate the effect of these factors on the evolutionary history of Chilean birds. We conducted a search in two bibliographic databases (PubMed and Scopus) over the period between 1998 and 2018 to identify the number and class of articles published in this research field. The quantification of specific research categories was also performed to assess progress in different molecular genetic issues of Chilean birds. Representative studies of the more active research areas: population structure, phylogeography, systematics and taxonomy and genetic diversity, were briefly commented on. Studies on genetic divergence analysis of cryptic species and the underlying genetics at molecular level of adaptive phenotypes in populations, were very scarce. Several types of mitochondrial and nuclear markers have been used, with COI plus D-loop and microsatellite loci, respectively, being the most widely-used markers. However, high-throughput analyses based on complete mitochondrial genomes have also been published. More than one hundred species have been analyzed; the most studied groups being penguins, followed by New World swallows. Although, to date, molecular genetic studies of Chilean birds still require further analysis, the studies available on some species or groups have provided important data to improve our understanding of the origin and evolution of this avifauna.

Gene pool sharing and genetic bottleneck effects in subpopulations of Eschweilera ovata (Cambess.) Mart. ex Miers (Lecythidaceae) in the Atlantic Forest of southern Bahia, Brazil

Forest loss and fragmentation are the main threats to the maintenance of the Atlantic Forest, an important global biodiversity hotspot. Because of the current critical level of deforestation, ecological corridors are needed to facilitate species dispersion and gene flow among fragments. This study was conducted to investigate the genetic variability and gene pool sharing of Eschweilera ovata in five forest remnants in southern Bahia, Brazil using nuclear simple sequence repeat (nSSR) and plastid simple sequence repeat (cpSSR) microsatellite markers. cpSSR marker analysis revealed the domains of four haplotypes, showing that 80% of the individuals had only four maternal origins, reflecting a founder effect and/or genetic bottleneck. The results of cpSSR and nSSR analyses indicated moderate genetic diversity, particularly in conservation units with full protection, which showed the best parameters of all areas evaluated. Another indication of the susceptibility of these populations to forest loss and fragmentation was the strong genetic bottleneck observed. In contrast, genetic structure analyses (FST and discriminant analysis of principal components) revealed gene pool sharing between the subpopulations, which may reflect the historical gene flow that occurred before forest fragmentation.