Bats are a diverse radiation of mammals of enduring interest for understanding the evolution of sensory specialization. Colour vision variation among species has previously been linked to roosting ...preferences and echolocation form in the suborder Yinpterochiroptera, yet questions remain about the roles of diet and habitat in shaping bat visual ecology. We sequenced OPN1SW and OPN1LW opsin genes for 20 species of leaf‐nosed bats (family Phyllostomidae; suborder Yangochiroptera) with diverse roosting and dietary ecologies, along with one vespertilionid species (Myotis lavali). OPN1LW genes appear intact for all species, and predicted spectral tuning of long‐wavelength opsins varied among lineages. OPN1SW genes appear intact and under purifying selection for Myotis lavali and most phyllostomid bats, with two exceptions: (a) We found evidence of ancient OPN1SW pseudogenization in the vampire bat lineage, and loss‐of‐function mutations in all three species of extant vampire bats; (b) we additionally found a recent, independently derived OPN1SW pseudogene in Lonchophylla mordax, a cave‐roosting species. These mutations in leaf‐nosed bats are independent of the OPN1SW pseudogenization events previously reported in Yinpterochiropterans. Therefore, the evolution of monochromacy (complete colour blindness) has occurred in both suborders of bats and under various evolutionary drivers; we find independent support for the hypothesis that obligate cave roosting drives colour vision loss. We additionally suggest that haematophagous dietary specialization and corresponding selection on nonvisual senses led to loss of colour vision through evolutionary sensory trade‐off. Our results underscore the evolutionary plasticity of opsins among nocturnal mammals.
Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust ...(tufted), were assigned to a single genus,
. Further, all tufted capuchins were assigned to a single species,
, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus,
, with eight currently recognized species and five
species, although these numbers are still under debate.
retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However,
elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (
; Cebus_imitator_1.0 and
GSC_monkey_1.0) facilitated large scale ascertainment of young lineage-specific
insertions. Reported here are 1607 capuchin specific and 678
specific
insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level
insertion polymorphisms. The
datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.
Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive ...attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.
Peripheral populations are valuable for conservation because of their potential genetic distinctiveness and ecological differentiation, but they tend to be smaller and more easily isolated than ...central populations. The Indochinese gray langurs living in the Wuliang Mountains of southwestern China, which form the northernmost peripheral population of the species, have ecological and behavioral features distinct from those of other such populations. We conducted semistructured interviews and field surveys on the population census and distribution of Indochinese gray langurs in Jingdong County from July 2013 to November 2013. These interviews provided the first large-scale data about the distribution and habitat use of these langurs; however, the group sizes estimated from interview reports were smaller than those obtained from direct counts. We estimate that 43 groups comprising
ca
. 1960 individual Indochinese gray langurs reside in evergreen broadleaf forests at an altitudinal distribution of 1700–2900 m in Jingdong. Of the 43 langur groups, 21 groups were observed outside the nature reserve or had estimated home ranges that straddle the boundary of the reserve. Because of the intensive conservation efforts to protect sympatric
Nomascus concolor
, hunting pressure on Indochinese gray langurs is minimal. However, the langur home ranges outside the nature reserve are not protected and remain threatened by deforestation for plantations (walnut, tea, etc.) and forest degradation caused by livestock grazing. More conservation attention than currently applied is needed to conserve langur groups living outside the reserve.
Abstract
Background: The ring-tailed lemur (Lemur catta) is a charismatic strepsirrhine primate endemic to Madagascar. These lemurs are of particular interest, given their status as a flagship ...species and widespread publicity in the popular media. Unfortunately, a recent population decline has resulted in the census population decreasing to <2,500 individuals in the wild, and the species's classification as an endangered species by the IUCN. As is the case for most strepsirrhine primates, only a limited amount of genomic research has been conducted on L. catta, in part owing to the lack of genomic resources. Results: We generated a new high-quality reference genome assembly for L. catta (mLemCat1) that conforms to the standards of the Vertebrate Genomes Project. This new long-read assembly is composed of Pacific Biosciences continuous long reads (CLR data), Optical Mapping Bionano reads, Arima HiC data, and 10X linked reads. The contiguity and completeness of the assembly are extremely high, with scaffold and contig N50 values of 90.982 and 10.570 Mb, respectively. Additionally, when compared to other high-quality primate assemblies, L. catta has the lowest reported number of Alu elements, which results predominantly from a lack of AluS and AluY elements. Conclusions: mLemCat1 is an excellent genomic resource not only for the ring-tailed lemur community, but also for other members of the Lemuridae family, and is the first very long read assembly for a strepsirrhine.
Black crested gibbons (Nomascus concolor) are 1 of only 3 gibbon species that have been observed in long‐term polygynous groups, but their mating behavior and reproductive characters have never been ...reported. Based on population monitoring over 7 years and direct observation for 26 months of the study groups in Wuliang Mountain, central Yunnan, we describe for the first time the copulation behavior and breeding pattern of free‐ranging western black crested gibbons. The gestation period of black crested gibbons is estimated to be between 6 and 7 months. The average breeding interval is 3.5 years, with infant independence at approximately 2.5 years. We observed 2 intra‐group copulations and 5 extra‐group copulations. Copulations were initiated when a female gave a ‘solicitation’ gesture. When a male made any mating attempt, the female might refuse it. These results demonstrate direct female mate choice. Both male and female gibbons dispersed from their natal groups and sometimes replaced paired adults in other groups. We observed no evidence of infanticide during inter‐group conflicts or after replacement of adults. Together with extra‐group copulations, these phenomena indicate a flexible social organization and complex mating system. We also observed a male‐biased sex ratio among offspring. More genetic work is necessary to describe the effects of inter‐group copulation and the genetic diversity of this population.
Fermentation preserves and transforms foods through autochthonous or introduced microorganisms. Fermentation is of special interest to ethnobiologists because it relies on place- and pracce-based ...knowledge, local flora and microbial taxa, is sensive to cultural and ecological conditions, and illuminates the interactions through which communities shape and are shaped by the world around them. In this short topical review, we discuss recent anthropological and ethnobiological research into fermentation, arguing that this topic deserves further attention during the current moment of microbial interest across social and natural sciences. We present a typology of scholarship on human-microbial relationships that delineates three intellectual camps in this literature: neo-cultural ecology, microbiopolitics, and the environmental humanities. In light of biomedical and scientific attention to microbes—not only as threats but also as complex and beneficial actors in our lives—it is crucial to understand how socioecological practices including growing, preparing, and consuming fermented foods sustain microbial communities, heritage foodways, and human wellbeing.
The semicircular canal system tracks head rotation and provides sensory input for the reflexive stabilization of gaze and posture. The purpose of this study was to investigate the intraspecific and ...intraindividual variation in the size of the three semicircular canals. The right and left temporal bones were extracted from 31 individuals of the short‐tailed shrew (Blarina brevicauda) and scanned on a high‐resolution x‐ray computed tomography system. The radius of curvature was calculated for each of the three semicircular canals for each side. Paired t‐tests and independent sample t‐tests indicated no significant differences in canal size between the right and left canals of the same individuals or between those of males and females of the same species. Pearson product moment correlation analyses demonstrated that there was no significant correlation between canal size and body mass in this sample.
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