High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox

Barcoding Brazilian mammals to monitor biological diversity and threats: Trends, perspectives, and knowledge gaps

DNA barcoding and environmental DNA (eDNA) represent significant advances for biomonitoring the world's biodiversity and its threats. However, these methods are highly dependent on the presence of species sequences on molecular databases. Brazil is one of the world's largest and most biologically diverse countries. However, many knowledge gaps still exist for describing, identifying, and monitoring of mammalian biodiversity using molecular methods. We aimed to unravel the patterns of the presence of Brazilian mammal species on molecular databases to improve our understanding of how effectively it would be to monitor them using DNA barcoding and environmental DNA, and contribute to mammalian conservation. We foundt many gaps in molecular databases, with many taxa being poorly represented, particularly from Amazonia, the order Lagomorpha, and arboreal, gomivorous, near extinct, and illegally traded species. Moreover, our analyses revealed that species description year was the most important factor determining the probability of a species to being sequenced. Primates are the group with the highest number of species considered a priority for sequencing due to their high level of combined threats. We highlight where investments are needed to fill knowledge gaps and increase the representativity of species on molecular databases to enable a better monitoring ability of Brazilian mammals encompassing different traits using DNA barcoding and environmental DNA.

From roads to biobanks: Roadkill animals as a valuable source of genetic data

To protect biodiversity we must understand its structure and composition including the bacteria and microparasites associated with wildlife, which may pose risks to human health. However, acquiring this knowledge often presents challenges, particularly in areas of high biodiversity where there are many undescribed and poorly studied species and funding resources can be limited. A solution to fill this knowledge gap is sampling roadkill (animals that die on roads as a result of collisions with circulating vehicles). These specimens can help characterize local wildlife and their associated parasites with fewer ethical and logistical challenges compared to traditional specimen collection. Here we test this approach by analyzing 817 tissue samples obtained from 590 roadkill vertebrate specimens (Amphibia, Reptilia, Aves and Mammalia) collected in roads within the Tropical Andes of Ecuador. First, we tested if the quantity and quality of recovered DNA varied across roadkill specimens collected at different times since death, exploring if decomposition affected the potential to identify vertebrate species and associated microorganisms. Second, we compared DNA stability across taxa and tissues to identify potential limitations and offer recommendations for future work. Finally, we illustrate how these samples can aid in taxonomic identification and parasite detection. Our study shows that sampling roadkill can help study biodiversity. DNA was recovered and amplified (allowing species identification and parasite detection) from roadkill even 120 hours after death, although risk of degradation increased overtime. DNA was extracted from all vertebrate classes but in smaller quantities and with lower quality from amphibians. We recommend sampling liver if possible as it produced the highest amounts of DNA (muscle produced the lowest). Additional testing of this approach in areas with different environmental and traffic conditions is needed, but our results show that sampling roadkill specimens can help detect and potentially monitor biodiversity and could be a valuable approach to create biobanks and preserve genetic data.

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outliers from a collection of gene trees is still missing. Here, we present PhylteR, a method that allows rapid and accurate detection of outlier sequences in phylogenomic datasets, i.e. species from individual gene trees that do not follow the general trend. PhylteR relies on DISTATIS, an extension of multidimensional scaling to 3 dimensions to compare multiple distance matrices at once. In PhylteR, these distance matrices extracted from individual gene phylogenies represent evolutionary distances between species according to each gene. On simulated datasets, we show that PhylteR identifies outliers with more sensitivity and precision than a comparable existing method. We also show that PhylteR is not sensitive to ILS-induced incongruences, which is a desirable feature. On a biological dataset of 14,463 genes for 53 species previously assembled for Carnivora phylogenomics, we show (i) that PhylteR identifies as outliers sequences that can be considered as such by other means, and (ii) that the removal of these sequences improves the concordance between the gene trees and the species tree. Thanks to the generation of numerous graphical outputs, PhylteR also allows for the rapid and easy visual characterization of the dataset at hand, thus aiding in the precise identification of errors. PhylteR is distributed as an R package on CRAN and as containerized versions (docker and singularity).

Pangolin Genomes Offer Key Insights and Resources for the World's Most Trafficked Wild Mammals

Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (∼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.

An evaluation of DNA extraction methods on historical and roadkill mammalian specimen

Guidelines identifying appropriate DNA extraction methods for both museum and modern biological samples are scarce or non-existent for mammalian species. Yet, obtaining large-scale genetic material collections are vital for conservation and management purposes. In this study, we evaluated five protocols making use of either spin-column, organic solvents, or magnetic bead-based methods for DNA extraction on skin samples from both modern, traffic-killed (n = 10) and museum (n = 10) samples of European hedgehogs, Ericaneus europaeus. We showed that phenol-chloroform or silica column (NucleoSpin Tissue) protocols yielded the highest amount of DNA with satisfactory purity compared with magnetic bead-based protocols, especially for museum samples. Furthermore, extractions using the silica column protocol appeared to produce longer DNA fragments on average than the other methods tested. Our investigation demonstrates that both commercial extraction kits and phenol-chloroform protocol retrieve acceptable DNA concentrations for downstream processes, from degraded remnants of traffic-killed and museum samples of mammalian specimens. Although all the tested methods could be applied depending on the research questions and laboratory conditions, commercial extraction kits may be preferred due to their effectiveness, safety and the higher quality of the DNA extractions.

When morphology does not fit the genomes: the case of rodent olfaction

Linking genes to phenotypes has been a major question in evolutionary biology for the last decades. In the genomic era, few studies attempted to link olfactory-related genes to different anatomical proxies. However, they found very inconsistent results. This study is the first to investigate a potential relation between olfactory turbinals and olfactory receptor (OR) genes. We demonstrated that despite the use of similar methodology in the acquisition of data, OR genes do not correlate with the relative and the absolute surface area of olfactory turbinals. These results challenged the interpretations of several studies based on different proxies related to olfaction and their potential relation to olfactory capabilities.

A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs

Estimates of wildlife population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples, particularly parent-offspring pairs. While these methods are similar to traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals are considered recaptured if a sample contains one or more close relatives. This makes methods based on genetically-identified parent-offspring pairs particularly interesting for species for which releasing marked animals back into the population is not desirable or not possible (e.g., harvested fish or game species). However, while these methods have successfully been applied in commercially important fish species, in the absence of life-history data, they are making several assumptions unlikely to be met for harvested terrestrial species. They assume that a sample contains only one generation of parents and one generation of juveniles of the year, while more than two generations can coexist in the hunting bags of long-lived species, or that the sampling probability is the same for each individual, an assumption that is violated when fecundity and/or survival depend on sex or other individual traits. In order to assess the usefulness of kin-based methods to estimate population sizes of terrestrial game species, we simulated population pedigrees of two different species with contrasting demographic strategies (wild boar and red deer), applied four different methods and compared the accuracy and precision of their estimates. We also performed a sensitivity analysis, simulating population pedigrees with varying fecundity characteristics and various levels of harvesting to identify optimal conditions of applicability of each method. We showed that all these methods reached the required levels of accuracy and precision to be effective in wildlife management under simulated circumstances (i.e., for species within a given range of fecundity and for a given range of sampling intensity), while being robust to fecundity variation. Despite the potential usefulness of the methods for terrestrial game species, care is needed as several biases linked to hunting practices still need to be investigated (e.g., when hunting bags are biased toward a particular group of individuals).

Comparison of the Genetic Diversity of the Captive and Wild Populations of the Tsushima Leopard Cat Using a GRAS-Di Analysis

Simple Summary

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) is exclusively found on the Tsushima Island in Japan; however, its population has been declining in recent years and is in danger of extinction. Hence, effort is underway for both in situ and ex situ conservation. Genetic management is also important in the management of captive populations, and various studies are being conducted regarding the same. In our previous study, we developed a reference genome of the Tsushima leopard cat and used GRAS-Di analysis, a genome-wide analysis, to genetically evaluate the wild populations. In this study, we attempted to improve the Tsushima leopard cat reference genome and compared the captive and wild populations by GRAS-di analysis. The results showed that the captive population had almost the same genetic diversity as the wild population and managed to remain in good condition.

Abstract

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) (TLC) is a regional population of the Amur leopard cat (P. bengalensis euptilurus) that lives only on the Tsushima Island in Japan and is threatened with extinction. Because the TLC population is small, genetic management is important. In this study, we obtained the draft genome of the TLC and identified single-nucleotide polymorphism (SNP) markers using a genotyping by random amplicon sequencing-direct (GRAS-Di) analysis. We genotyped 31 captive individuals and 50 wild individuals, of which 48 were from a previous study. The identified SNPs were used to clarify the genetic diversity and genetic structure of the wild and captive populations of the TLC. The size of the genome was estimated to be about 2.42 Gb. The number of SNP markers developed was 139, and although PID and probability of exclusion obtained using these SNP markers were not as high as those reported in the studies of other wild species, these SNP markers could be used to identify individuals and parentage. Moreover, the genetic diversity indices of the captive population were similar to those of the wild population. These SNP markers will be useful for understanding the ecology of the TLC and planning conservation strategies.

Genomic evidence for the parallel regression of melatonin synthesis and signaling pathways in placental mammals

Background: The study of regressive evolution has yielded a wealth of examples where the underlying genes bear molecular signatures of trait degradation, such as pseudogenization or deletion. Typically, it appears that such disrupted genes are limited to the function of the regressed trait, whereas pleiotropic genes tend to be maintained by natural selection to support their myriad purposes. One such set of pleiotropic genes is involved in the synthesis ( AANAT, ASMT) and signaling ( MTNR1A, MTNR1B) of melatonin, a hormone secreted by the vertebrate pineal gland. Melatonin provides a signal of environmental darkness, thereby influencing the circadian and circannual rhythmicity of numerous physiological traits. Therefore, the complete loss of a pineal gland and the underlying melatonin pathway genes seems likely to be maladaptive, unless compensated by extrapineal sources of melatonin. Methods: We examined AANAT, ASMT, MTNR1A and MTNR1B in 123 vertebrate species, including pineal-less placental mammals and crocodylians. We searched for inactivating mutations and modelled selective pressures (dN/dS) to test whether the genes remain functionally intact. Results: We report that crocodylians retain intact melatonin genes and express AANAT and ASMT in their eyes, whereas all four genes have been repeatedly inactivated in the pineal-less xenarthrans, pangolins, sirenians, and whales. Furthermore, colugos have lost these genes, and several lineages of subterranean mammals have partial melatonin pathway dysfunction. These results are supported by the presence of shared inactivating mutations across clades and analyses of selection pressure based on the ratio of non-synonymous to synonymous substitutions (dN/dS), suggesting extended periods of relaxed selection on these genes. Conclusions: The losses of melatonin synthesis and signaling date to tens of millions of years ago in several lineages of placental mammals, raising questions about the evolutionary resilience of pleiotropic genes, and the causes and consequences of losing melatonin pathways in these species.

High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox

In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.