Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction

Bending the curve of global freshwater biodiversity loss: what are the prospects?

Freshwater biodiversity conservation has received substantial attention in the scientific literature and is finally being recognized in policy frameworks such as the Global Biodiversity Framework and its associated targets for 2030. This is important progress. Nonetheless, freshwater species continue to be confronted with high levels of imperilment and widespread ecosystem degradation. An Emergency Recovery Plan (ERP) proposed in 2020 comprises six measures intended to "bend the curve" of freshwater biodiversity loss, if they are widely adopted and adequately supported. We review evidence suggesting that the combined intensity of persistent and emerging threats to freshwater biodiversity has become so serious that current and projected efforts to preserve, protect and restore inland-water ecosystems may be insufficient to avert substantial biodiversity losses in the coming decades. In particular, climate change, with its complex and harmful impacts, will frustrate attempts to prevent biodiversity losses from freshwater ecosystems already affected by multiple threats. Interactions among these threats will limit recovery of populations and exacerbate declines resulting in local or even global extinctions, especially among low-viability populations in degraded or fragmented ecosystems. In addition to impediments represented by climate change, we identify several other areas where the absolute scarcity of fresh water, inadequate scientific information or predictive capacity, and a widespread failure to mitigate anthropogenic stressors, are liable to set limits on the recovery of freshwater biodiversity. Implementation of the ERP rapidly and at scale through many widely dispersed local actions focused on regions of high freshwater biodiversity and intense threat, together with an intensification of ex-situ conservation efforts, will be necessary to preserve native freshwater biodiversity during an increasingly uncertain climatic future in which poorly understood, emergent and interacting threats have become more influential. But implementation of the ERP must be accompanied by measures that will improve water, energy and food security for humans - without further compromising the condition of freshwater ecosystems. Unfortunately, the inadequate political implementation of policies to arrest widely recognized environmental challenges such as climate change do not inspire confidence about the possible success of the ERP. In many parts of the world, the Anthropocene future seems certain to include extended periods with an absolute scarcity of uncontaminated surface runoff that will inevitably be appropriated by humans. Unless there is a step-change in societal awareness of - and commitment to - the conservation of freshwater biodiversity, together with necessary actions to arrest climate change, implementation of established methods for protecting freshwater biodiversity may not bend the curve enough to prevent continued ecosystem degradation and species loss.

Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot

Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.

How Can Genomics Help or Hinder Wildlife Conservation?

Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.

Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang)

Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.

Molecular Assessments, Statistical Effectiveness Parameters and Genetic Structure of Captive Populations of Tursiops truncatus Using 15 STRs

Simple Summary

The bottlenose dolphins are one of the most used species in entertainment, assisted therapy, education, and research on welfare. However, their maintenance in captivity requires powerful and sensitive tools for preserving their diversity. The number of genetic markers for this purpose remains controversial, restraining the marine species’ genetic diversity determination. We aimed to select 15 hypervariable molecular markers whose statistical parameters were made in 210 captive dolphins from 18 Mexican centers to support their usefulness. The proposed set of markers allowed us to obtain a genetic fingerprint of each dolphin. Additionally, we identified the structure of the captive population, analyzing the groups according to the capture location. Such characterization is key for maintaining the captive species’ biodiversity rates within conservation and reintroduction programs. However, these 15 genetic markers can also be helpful for small- isolated populations, subspecies and other genera of endangered and vulnerable species.

Abstract

Genetic analysis is a conventional way of identifying and monitoring captive and wildlife species. Knowledge of statistical parameters reinforcing their usefulness and effectiveness as powerful tools for preserving diversity is crucial. Although several studies have reported the diversity of cetaceans such as Tursiops truncatus using microsatellites, its informative degree has been poorly reported. Furthermore, the genetic structure of this cetacean has not been fully studied. In the present study, we selected 15 microsatellites with which 210 dolphins were genetically characterized using capillary electrophoresis. The genetic assertiveness of this set of hypervariable markers identified one individual in the range of 6.927e¹³ to 1.806e¹⁶, demonstrating its substantial capability in kinship relationships. The genetic structure of these 210 dolphins was also determined regarding the putative capture origin; a genetic stratification (k = 2) was found. An additional dolphin group of undetermined origin was also characterized to challenge the proficiency of our chosen markers. The set of markers proposed herein could be a helpful tool to guarantee the maintenance of the genetic diversity rates in conservation programs both in Tursiops truncatus and across other odontocetes, Mysticeti and several genera of endangered and vulnerable species.