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.

Leptospira borgptersenii and Leptospira interrogans identified in wild mammals in Rio Grande do Sul, Brazil.

Leptospira spp. are bacteria responsible for leptospirosis, a zoonotic disease with considerable impacts on the economy, animal health, and public health. This disease has a global distribution and is particularly prevalent in Brazil. Both rural and urban environments are habitats for Leptospira spp., which are primarily transmitted through contact with the urine of infected animals. Consequently, domestic and wild species can harbor these prokaryotes and serve as infection sources for other hosts. In the context of wild animals, there is a dearth of molecular studies elucidating the roles of various animal and bacterial species in the epidemiology of leptospirosis. Therefore, this study aimed to evaluate the presence of Leptospira spp. DNA in different species of free-living and captive wild animals and to assess the phylogenetic relationships of the identified microorganisms in Rio Grande do Sul, Brazil. The samples were evaluated for the presence of the gene lipL32 by polymerase chain reaction (PCR) and sequencing of the amplified fragment after which phylogenetic analyzes were carried out. DNA from Leptospira spp. was extracted from kidney tissue from wild animals (Mammalia class). Pathogenic Leptospira spp. DNA was detected in 9.6% (11/114) of the samples, originating from nine species of wild animals, including the white-eared opossum (Didelphis albiventris), skunk (Conepatus chinga), geoffroy's cat (Leopardus geoffroyi), margay (Leopardus wiedii), pampas fox (Lycalopex gymnocercus), capybara (Hydrochoerus hydrochaeris), common marmoset (Callithrix jacchus), neotropical river otter (Lontra longicaudis), and european hare (Lepus europaeus). Phylogenetic analysis revealed the presence of Leptospira borgpetersenii and Leptospira interrogans in these animals. This research is the first study contributing to the epidemiology of leptospirosis by identifying L. borgpetersenii and L. interrogans in free-living and captive wild animals in Rio Grande do Sul, Brazil, potentially acting as bacterial reservoirs. Additionally, our findings can inform sanitary measures for controlling and preventing the disease, thereby safeguarding public health.

Checklist of hosts, illustrated geographical range, and ecology of tick species from the genus Ixodes (Acari, Ixodidae) in Russia and other post-Soviet countries.

Hard ticks (Acari: Ixodidae) are the economically and ecologically most important blood-sucking arthropod vectors that can transmit disease agents under temperate climate. In this group, the highest number of species (currently nearing 270) belongs to the genus Ixodes. For this review, more than 400 papers related to this genus in the context of Russia were checked for data on the host records, locations of collection, as well as ecology of assigned tick species. This monograph compensates for the lack of a similarly comprehensive English-language overview of Ixodes species in the region of Russia for nearly half century, and also makes a large set of data easily available for international readers, which is especially important if the original source is difficult to access from outside this country. In addition, the data from a significant number of papers on this topic available only in the Russian language are made accessible through this work.

Hypercanines: Not just for sabertooths.

Hypercanines are here defined as hypertrophied caniniform teeth, that is, canine teeth that are elongated to serve specific functions in different clades of mammals and their synapsid ancestors. This article presents an overview of the occurrence of hypercanines, their growth, and their function across a broad range of clades. Sabertooth felids and felid-like taxa are found to be unique in having determinate growth (although some Dinocerata may also have this). The most common function of hypercanines among herbivores is found to be sexual display and male-male competition. Three clades of small ruminants have evolved hypercanines that can move within their sockets, although the evolutionary details behind this convergent adaptation have not been worked out.

Site occupation and range expansion by the endangered, Mexican microendemic San Quintín Kangaroo Rat (Dipodomys gravipes).

The San Quintin Kangaroo Rat, a rodent species microendemic to the San Quintin-El Rosario region in Baja California that was considered potentially extinct in the wild, was recently rediscovered. This stimulated subsequent searches by us throughout its known distribution range and on sites that seemed suitable beyond its limits. We captured the species at 19 out of 42 localities surveyed, of which 6 are beyond its historically known distribution range, expanding the latter by ~60 km. Most sites occupied by the species occur on abandoned farmland in early ecological successional stages. Our data support that in the highly transformed agricultural landscape into which the region was converted in the 20th century, the species was able to survive undetected and colonize/recolonize sites once habitat became adequate after agricultural abandonment. This exhibits that the species is highly resilient and persisted as a metapopulation. Further research and conservation actions must be framed within context of the region's agricultural development.

Quintín­El Rosario, Baja California, considerada potencialmente extinta, se redescubrió recientemente. Ello estimuló búsquedas en todo su rango de distribución conocido y en sitios potenciales que parecían adecuados más allá de sus límites geográficos. Capturamos a la especie en 19 de 42 localidades, de las cuales 6 estaban fuera de su rango de distribución históricamente conocido, expandiendo este rango en ~60 km. La mayoría de los sitios ocupados por la especie se encuentran en tierras de cultivo abandonadas en etapas tempranas de sucesión ecológica. Nuestros datos respaldan la hipótesis de que el paisaje agrícola altamente antropizado, en el que se convirtió la región en el siglo XX, la especie sobrevivió en refugios y colonizó/recolonizó sitios una vez que el hábitat se volvió adecuado después de su abandono agrícola. Esto mostró que la especie es altamente resiliente y persistió como una metapoblación. Las futuras acciones de investigación y conservación deben enmarcarse en el contexto del desarrollo agrícola de la región.

A Global Systematic Review of Lead (Pb) Exposure and its Health Effects in Wild Mammals.

Lead (Pb) is a toxic nonessential metal, known mainly for causing poisoning of humans and wild birds. However, little is known about Pb exposure and its associated health effects in wild mammals. We conducted a global systematic literature review to identify peer-reviewed studies published on Pb exposure in wild mammalian species and the health effects they identified. In total, 183 studies, conducted in 35 countries and published over 62 yr (1961-2022), were included in the review. Only 6% (11/183) of the studies were conducted in developing countries. Although 153 mammalian species were studied, most studies focused on species that are easy to access (i.e., hunted species and small mammals that are easy to trap). Therefore, carnivores and scavengers were less frequently studied than herbivores and omnivores. Despite all studies reporting Pb concentrations, only 45 (25%) studies investigated health effects and, of these 45 studies, only 28 (62%) found any health effect in 57 species. All health effects were negative and ranged from subclinical effects to fatality. Methodologies of Pb sampling and quantification and reporting of results varied widely across the studies, making both Pb concentrations and health effects difficult to compare and evaluate. Thus, there is a need for more research on Pb exposure and its health effects on wild mammals, especially as carnivores and scavengers could be used as sentinels for ecosystem health.

Speciation on the Roof of the World: Parallel Fast Evolution of Cryptic Mole Vole Species in the Pamir-Alay-Tien Shan Region.

Speciation is not always accompanied by morphological changes; numerous cryptic closely related species were revealed using genetic methods. In natural populations of Ellobius tancrei (2n = 54-30) and E. alaicus (2n = 52-48) of the Pamir-Alay and Tien Shan, the chromosomal variability due to Robertsonian translocations has been revealed. Here, by comprehensive genetic analysis (karyological analyses as well as sequencing of mitochondrial genes, cytb and COI, and nuclear genes, XIST and IRBP) of E. alaicus and E. tancrei samples from the Inner Tien Shan, the Alay Valley, and the Pamir-Alay, we demonstrated fast and independent diversification of these species. We described an incompletely consistent polymorphism of the mitochondrial and nuclear markers, which arose presumably because of habitat fragmentation in the highlands, rapid karyotype changes, and hybridization of different intraspecific varieties and species. The most intriguing results are a low level of genetic distances calculated from mitochondrial and nuclear genes between some phylogenetic lines of E. tancrei and E. alaicus, as well significant species-specific chromosome variability in both species. The chromosomal rearrangements are what most clearly define species specificity and provide further diversification. The "mosaicism" and inconsistency in polymorphism patterns are evidence of rapid speciation in these mammals.

The Diversity of Small Mammals along a Large River Valley Revealed from Pellets of Tawny Owl Strix aluco.

The Vistula River is one of the largest European semi-natural rivers of high ecological value that functions as an ecological corridor. To assess the structure of small mammal communities along the Vistula River, an analysis of the diet of an opportunistic predator, the tawny owl Strix aluco, was used. A total of 6355 individuals of 19 species were found, including 5 soricomorph species, 12 rodents, 1 carnivore, and 1 bat species. Tawny owls most frequently caught Apodemus agrarius, Clethrionomys glareolus, Apodemus flavicollis, and Microtus arvalis. Rodents dominated small mammal communities (90%), followed by soricomorphs (8%), and the share of Chiroptera was significant (2%). Using Ward's method in cluster analysis, three clusters of sites with similar mammal communities were identified. The cluster that included 17 study sites with the dominance of agriculture habitats was inhabited by diverse mammal communities with a high number of species. In the cluster composed of three suburban forest sites, mammal communities had the lowest diversity, although the high species richness and the highest shares of the forest species (A. flavicollis, C. glareolus, and Nyctalus noctula). Mammal communities in the cluster were composed of three urban sites were dominated by A. agrarius and M. arvalis. The study indicates the high species richness of small mammals in floodplains of the Vistula River and the adjacent areas in central Poland. The floodplain offers suitable habitats for species associated with forests, water bodies, agricultural land, and developed areas. The data collected confirms earlier model predictions about the presence of well-connected local populations of forest mammals along the Vistula River.

A NEW EIMERIAN (APICOMPLEXA: EIMERIIDAE) FROM EASTERN MOLE, SCALOPUS AQUATICUS (MAMMALIA: EULIPOTYPHLA: TALPIDAE), IN CENTRAL ARKANSAS, WITH ADDITIONAL INFORMATION ON CYCLOSPORA YATESI MCALLISTER, MOTRIUK-SMITH, AND KERR.

The eastern mole, Scalopus aquaticus (L.), is a common inhabitant of loamy soils in Canada, the eastern United States, and Mexico. Seven coccidian parasites have been previously reported from S. aquaticus, including 3 cyclosporans and 4 eimerians from hosts taken in Arkansas and Texas. A single S. aquaticus, collected in February 2022 in central Arkansas, was found to be passing oocysts of 2 coccidians, a new species of Eimeria, and Cyclospora yatesiMcAllister, Motriuk-Smith, and Kerr, 2018. Oocysts of Eimeria brotheri n. sp. are ellipsoidal (sometimes ovoidal) with a smooth bilayered wall, measure 14.0 × 9.9 µm, and have a length/width (L/W) ratio of 1.5; both micropyle and oocyst residua are absent, but a single polar granule is present. Sporocysts are ellipsoidal and measure 8.1 × 4.6 µm, L/W 1.8; a flattened to knoblike Stieda body as well as a rounded sub-Stieda body are present. The sporocyst residuum is composed of an irregular mass of large granules. Additional metrical and morphological information is provided on oocysts of C. yatesi. This study demonstrates that although several coccidians were previously documented from this host, additional S. aquaticus should be examined for coccidians from Arkansas as well as other parts of its range.

Morphological and molecular confirmation of Ornithodoros hasei (Schulze, 1935) (Acari: Argasidae) in Colombia.

A large number of tick species are proven vectors for the transmission of bacteria, protozoa, and viruses. Soft ticks (Acari: Argasidae) in South America have been found to be the most frequent carriers of borreliae of the relapsing fever group (RFG); however, there are several information gaps specially on the taxonomy and distribution of some tick species. Here, we used light microscopy, scanning electron microscopy, and PCR amplification of a fragment of the mitochondrial 16S rRNA gene to evaluate 174 larvae of Ornithodoros (Argasidae) collected from three bat species (Eptesicus orinocensis, Molossus rufus and Noctilio albiventris) in the Orinoquia Region of Colombia. The morphological and molecular results confirmed that all the analyzed larvae corresponded to Ornithodoros hasei. Comparisons of mitochondrial 16S rDNA sequences showed low genetic divergence (0% - 0.3%) between larvae of the Department of Arauca in the Orinoquia Region and higher genetic divergence (3.4 - 4.7%) in sequences from other American countries. Our work represents the most recent collection of this species in Colombia and provides a molecular evaluation for the first time. Moreover, a new association of O. hasei with bats such as E. orinocensis is documented. Considering the wide distribution of O. hasei in the American Continent, and its putative role as vector for Borrelia, integrative studies that involve morphological, morphometric, molecular data and experimental crosses are needed to determine if the higher genetic distances are associated with cryptic speciation, as detected in other tick complexes, or represent genetic divergences among geographically different populations of O. hasei.

At the root of the mammalian mind: The sensory organs, brain and behavior of pre-mammalian synapsids.

All modern mammals are descendants of the paraphyletic non-mammaliaform Synapsida, colloquially referred to as the "mammal-like reptiles." It has long been assumed that these mammalian ancestors were essentially reptile-like in their morphology, biology, and behavior, i.e., they had a small brain, displayed simple behavior, and their sensory organs were unrefined compared to those of modern mammals. Recent works have, however, revealed that neurological, sensory, and behavioral traits previously considered typically mammalian, such as whiskers, enhanced olfaction, nocturnality, parental care, and complex social interactions evolved before the origin of Mammaliaformes, among the early-diverging "mammal-like reptiles." In contrast, an enlarged brain did not evolve immediately after the origin of mammaliaforms. As such, in terms of paleoneurology, the last "mammal-like reptiles" were not significantly different from the earliest mammaliaforms. The abundant data and literature published in the last 10 years no longer supports the "three pulses" scenario of synapsid brain evolution proposed by Rowe and colleagues in 2011, but supports the new "outside-in" model of Rodrigues and colleagues proposed in 2018, instead. As Mesozoic reptiles were becoming the dominant taxa within terrestrial ecosystems, synapsids gradually adapted to smaller body sizes and nocturnality. This resulted in a sensory revolution in synapsids as olfaction, audition, and somatosensation compensated for the loss of visual cues. This altered sensory input is aligned with changes in the brain, the most significant of which was an increase in relative brain size.

Mammalian forelimb evolution is driven by uneven proximal-to-distal morphological diversity.

Vertebrate limb morphology often reflects the environment due to variation in locomotor requirements. However, proximal and distal limb segments may evolve differently from one another, reflecting an anatomical gradient of functional specialization that has been suggested to be impacted by the timing of development. Here, we explore whether the temporal sequence of bone condensation predicts variation in the capacity of evolution to generate morphological diversity in proximal and distal forelimb segments across more than 600 species of mammals. Distal elements not only exhibit greater shape diversity, but also show stronger within-element integration and, on average, faster evolutionary responses than intermediate and upper limb segments. Results are consistent with the hypothesis that late developing distal bones display greater morphological variation than more proximal limb elements. However, the higher integration observed within the autopod deviates from such developmental predictions, suggesting that functional specialization plays an important role in driving within-element covariation. Proximal and distal limb segments also show different macroevolutionary patterns, albeit not showing a perfect proximo-distal gradient. The high disparity of the mammalian autopod, reported here, is consistent with the higher potential of development to generate variation in more distal limb structures, as well as functional specialization of the distal elements.

Revising the diversity within the Dwarf Dog-faced Bat, Molossopstemminckii (Chiroptera, Molossidae), with the revalidation of the endangered Molossopsgriseiventer.

The genus Molossops includes two monotypic species of insectivore bats distributed in South America: Molossopsneglectus and Molossopstemminckii. Both can be differentiated, based on sizes, M.temminckii being smaller (forearm less than 33 mm). Despite being monotypic, at least two additional subspecies have been described for M.temminckii, of which M.temminckiigriseiventer from the inter-Andean Valley of the Magdalena River in Colombia might represent a valid taxon. To test the taxonomic status of M.t.griseiventer, we reviewed specimens of M.temminckii from cis- and trans-Andean localities in Colombia. We used Cytochrome-b and Cytochrome Oxidase I comparisons to test the phylogenetic position of cis- and trans-Andean samples and compared qualitative morphology, morphometric and bioacoustics. Our results show that M.t.griseiventer is differentiated from cis-Andean specimens, providing further evidence of its validity at the species level. Furthermore, M.temminckii (sensu stricto) is also distributed in Colombia, but both M.griseiventer and M.temminckii are allopatric, with the Andes acting as a barrier. The specific identity of the specimens from the Caribbean Region of Colombia needs a new evaluation, but our results clearly show that the diversity of Molossops is underestimated.

Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework.

Terrestrial mammals face a severe crisis of habitat loss worldwide. Therefore, assessing information on habitat loss throughout different time periods is crucial for assessing species' conservation statuses based on the IUCN Red List system. To support the national extinction risk assessment in Brazil (2016-2022), we developed a script that uses the MapBiomas Project 6.0 data source of land cover and land use (annual maps at 30 m scale) within the Google Earth Engine (GEE) platform to calculate habitat loss. We defined suitable habitats from the MapBiomas Project land cover classification for 190 mammalian taxa, according to each species range map and ecological characteristics. We considered a period of three generation lengths to assess habitat loss in accordance with the Red List assessment criteria. We used the script to estimate changes in available habitat throughout the analyzed period within the species' known ranges. The results indicated that habitat loss occurred within 94.3% of the analyzed taxa range, with the Carnivora order suffering the greatest habitat loss, followed by the Cingulata order. These analyses may be decisive for applying criteria, defining categories during the assessment of at least 17 species (9%), enriching discussions, and raising new questions for several other species. We considered the outcome of estimating habitat loss for various taxa when applying criterion A, which refers to population reduction, thus supporting more accurate inferences about past population declines.

Rostrum morphology and feeding strategy of the baleen whale indicate that right whales and pygmy right whales became skimmers independently.

Baleen whales have lost their functional teeth and begun to use their baleen plates to feed on small prey. Modern baleen whales exhibit different types of feeding strategies, such as lunging, skimming and so on. The evolution of feeding strategy in the Chaeomysticeti is an important step in considering niche partitioning and diversification, feeding efficiency and gigantism, and evolution and extinction. This study analyses the rostrum morphology to test the hypothesis that specific rostral morphologies facilitate special feeding strategies, using modern species and their observed feeding strategies. By this means, the convergence of rostral morphology can be recognized in the closest groups in the morphospace. As a result, the two linages (Balaenidae and Caperea marginata) are recognized to have convergent rostral morphology. In addition, an early member of the Chaeomysticeti, Yamatocetus canaliculatus, and most fossil species are plotted in or close to the cluster of lunge feeders. The original feeding strategy of the Chaeomysticeti could be more similar to lunge feeding than to skim feeding. Fossil relatives of the two linages showing transitional conditions indicate that they shifted to skim feeding independently. The evolution of the feeding strategy of the Chaeomysticeti is possibly more complex than that was thought.

Diversity and Relative Abundance of Ungulates and Other Medium and Large Mammals in Flooded Forests in the Dahomey Gap (Togo).

"The Dahomey Gap" is a human-derived mostly savannah region that separates the Guineo-Congolian rainforest block into two major units: the Upper Guinean and the Lower Guinean Forest blocks. Several forest patches are distributed throughout this savannah-dominated habitat. The mammal communities in the Dahomey Gap region have been poorly studied. In this paper we analyse the species richness and abundance of, as well as conservation implications for, medium and large mammals (especially ungulates) inhabiting a complex of flooded forests near the Mono river in south-eastern Togo. We use several field methods to describe the species richness of mammals in this area, including camera-trapping, recce transects, Kilometric Index of Abundance (KIA) estimates, examination of hunters' catches and face-to-face hunter interviews. Overall, we directly recorded 19 species that coexist in these forests. Based on interviews, nine other species were confirmed as present in the study area. Only five species were common: Cephalophus rufilatus, Tragelaphus scriptus, Chlorocebus aethiops, Atilax paludinosus and Herpestes ichneumon. The area still contains various threatened species such as Tragelaphus spekii and Hippopotamus amphibius. We stress that to ensure the protection of the Dahomey Gap mammals, it is important to seriously consider protecting not only the forest patches but also the surroundings, mainly savannah landscapes.

The anteriorization of tooth position underlies the atavism of tooth morphology: Insights into the morphogenesis of mammalian molars.

The evolution and development of complex molars as a key innovation in mammals have long been of interest yet remain poorly understood. With reference to century-old theories and modern findings, we focused on the teeth of pinnipeds (Carnivora) and cetaceans (Cetartiodactyla), which are morphologically simple compared with those of other mammals, and thus can be considered a reversal toward the ancestral state of nonmammalian synapsids. By reconstructing the evolutionary history of tooth complexity for the phylogenies of Carnivora and Cetartiodactyla, we established that a secondary evolution of simple teeth from more complex molars has occurred independently multiple times. Our phylogenetic comparative analyses showed that a simplification in tooth morphology was correlated with a more anterior dentition position relative to the component bones of the upper jaw in both Carnivora and Cetartiodactyla. These results suggest that the anterior shift of tooth position relative to the morphogenetic fields present in the jaw contributed to the evolutionary simplification in molar morphology. Our findings provide insights into the developmental basis of complex mammalian dentition.

Sexual selection leads to positive allometry but not sexual dimorphism in the expression of horn shape in the blue wildebeest, Connochaetes taurinus.

Sexual selection is thought to be an important driver of adaptation, speciation and extinction. Empirically testing these predictions across macroevolutionary timescales first requires an understanding of the morphology of secondary sexual traits in extant taxa. We used three-dimensional geometric morphometrics to analyse a large sample of the skull of the blue wildebeest, Connochaetes taurinus, in which horns are found in both sexes but only used in intrasexual competition in males. We show that the horns fit several predictions of secondary sexual traits; overall skull shape is significantly correlated with size (R2 = 0.38, p = 0.001), and the sexually selected horns show drastically higher growth rates and variation than any other skull element, supporting previous findings. We also find that despite showing significant sexual dimorphism in shape and size (R2 = 0.21, p = 0.001), allometric growth trajectories of sexes are identical (R2 = 0.01, p = 0.635) and dimorphism is not readily detectable without prior knowledge of sex, and is not possible when shape is corrected for size. Our results show that even with strong sexual selection operating in only one sex, the expression of secondary sexual traits may show characteristic and indistinguishable patterns of growth and variance in both sexes.

Ovarian Filariasis in a Wild Southern Tamandua (Tamanduatetradactyla; Mammalia: Myrmecophagidae).

Knowledge of reproductive health in wild southern tamanduas (Tamandua tetradactyla; Mammalia: Myrmecophagidae) is fragmentary. During necropsies of roadkill xenarthran species in Brazil, a case of ovarian filariasis in an adult female southern tamandua was observed. Macroscopically, both ovaries were irregularly enlarged and had numerous smooth protuberances. Histologically, the affected ovarian parenchyma presented adult nematodes (including females with microfilaria) surrounded by pleocellular inflammatory infiltrates. The morphological characteristics of the nematodes were consistent with the superfamily Filarioidea (order Spirurida). The adjacent ovarian parenchyma had developing and atretic follicles at different stages of maturation. Filarial nematodes were not observed in other tissues. The cause of death of this tamandua was fatal acute polytrauma as a consequence of the motor vehicle collision. This case adds to a prior report of ovarian filariasis in two southern tamanduas in Nicaragua and Guatemala, dating back almost 100 years, and suggests filarial infections could potentially have an impact on reproductive success in southern tamanduas and possibly other xenarthrans. Several xenarthran species are under different levels of threat and knowledge of their basic reproductive health is crucial for conservation programs.