skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: How genomic insights into the evolutionary history of clouded leopards inform their conservation
Clouded leopards (Neofelisspp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comprehensive investigation of the whole genomes, population genetics, and adaptive evolution ofNeofelis. Our results indicate the genusNeofelisarose during the Pleistocene, coinciding with glacial-induced climate changes to the distributions of savannas and rainforests, and signatures of natural selection associated with genes functioning in tooth, pigmentation, and tail development, associated with clouded leopards’ unique adaptations. Our study highlights high-altitude adaptation as the main factor driving nontaxonomic population differentiation inNeofelis nebulosa. Population declines and inbreeding have led to reduced genetic diversity and the accumulation of deleterious variation that likely affect reproduction of clouded leopards, highlighting the urgent need for effective conservation efforts.  more » « less
Award ID(s):
1753760
PAR ID:
10474111
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publisher / Repository:
AAAS
Date Published:
Journal Name:
Science Advances
Volume:
9
Issue:
40
ISSN:
2375-2548
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ABSTRACT Alzheimer's disease (AD) and its associated pathology have been primarily identified in humans, who have relatively large brains and long lifespans. To expand what is known about aging and neurodegeneration across mammalian species, we characterized amyloid‐beta (Aβ) and tau lesions in five species of aged felids (n= 9; cheetah, clouded leopard, African lion, serval, Siberian tiger). We performed immunohistochemistry to detect Aβ40 and Aβ42 in plaques and vessels and hyperphosphorylated tau in the temporal lobe gyrus sylvius and in the CA1 and CA3 subfields of the hippocampus. We also quantified the densities and morphological types of microglia expressing IBA1. We found that diffuse Aβ42 plaques, but not dense‐core plaques, were present more frequently in the temporal cortex and tended to be more common than Aβ40 plaques across species. Conversely, vascular Aβ was labeled more consistently with Aβ40 for each species on average. Although all individuals showed some degree of Aβ40 and/or Aβ42 immunoreactivity, only the cheetahs and clouded leopards exhibited intraneuronal hyperphosphorylated tau (i.e., pretangles), which was more common in the hippocampus. Reactive, intermediate microglia were significantly associated with total Aβ40 vessel area and pretangle load in the hippocampus. This study demonstrates the co‐occurrence of Aβ and tau pathology in two felid species, cheetahs and clouded leopards. Overall, these results provide an initial view of the manifestation of Aβ and tau pathology in aged, large‐brained felids, which can be compared with markers of neurodegeneration across different taxa, including domestic cats, nonhuman primates, and humans. 
    more » « less
  2. Gilbert, Jack A (Ed.)
    Colpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining ofColpodamitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically revealsColpodaciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms. 
    more » « less
  3. Abstract Specialist insects are especially susceptible to loss of genetic diversity in the face of habitat destruction and fragmentation. Implementing effective conservation practices for specialist insects will benefit from knowledge of population structure and genetic diversity. Because insects are hyper-diverse, characterizing the population structure of all species within the insect community is untenable, even if focused within a particular habitat type. Thus, concentrating on a single species specialized to a particular habitat type is needed to infer general trends. Here, we investigate the range-wide population genetics ofTetraopes texanusHorn 1878 (Coleoptera: Cerambycidae), which provides a useful model of grassland insects due to its’ habitat specificity and unique biology.Tetraopes texanusoccurs primarily in Texas and Oklahoma, into Northern Mexico, and possibly into eastern New Mexico but also occurs in Black Belt prairies of Mississippi and Alabama. Mitochondrial and nuclear DNA (RAD-seq) analysis identified two distinct population clusters ofT. texanuscorresponding to the Texas and Oklahoma population and the Mississippi and Alabama population. Demographic models indicate ongoing, though incomplete, isolation of the two populations, with estimated dates of divergence in the mid-Pleistocene, coinciding with the end of a glacial period and a shift in glacial interval. These results can inform conservation of grassland adapted insects and offers insight to the biogeography of the Gulf Coastal Plain. 
    more » « less
  4. Summary Replicated trait evolution can provide insights into the mechanisms underlying the evolution of biodiversity. One example of replicated evolution is the awn, an organ elaboration in grass inflorescences.Awns are likely homologous to leaf blades. We hypothesized that awns have evolved repeatedly because a conserved leaf blade developmental program is continuously activated and suppressed over the course of evolution, leading to the repeated emergence and loss of awns. To evaluate predictions arising from our hypothesis, we used ancestral state estimations, comparative genetics, anatomy, and morphology to trace awn evolution.We discovered that awned lemmas that evolved independently share similarities in developmental trajectory. In addition, in two species with independently derived awns and differing awn morphologies (Brachypodium distachyonandAlopecurus myosuroides), we found that orthologs of theYABBYtranscription factor geneDROOPING LEAFare required for awn initiation. Our analyses of awn development inBrachypodium distachyon,Alopecurus myosuroides, andHolcus lanatusalso revealed that differences in the relative expansion of awned lemma compartments can explain diversity in awn morphology at maturity.Our results show that developmental conservation can underlie replicated evolution and can potentiate the evolution of morphological diversity. 
    more » « less
  5. Abstract Droughts are increasing in frequency and severity globally due to climate change, leading to changes in resource availability that may have cascading effects on animal ecology. Resource availability is a key driver of animal space use, which in turn influences interspecific interactions like intraguild competition. Understanding how climate‐induced changes in resource availability influence animal space use, and how species‐specific responses scale up to affect intraguild dynamics, is necessary for predicting broader community‐level responses to climatic changes.Although several studies have demonstrated the ecological impacts of drought, the behavioural responses of individuals that scale up to these broader‐scale effects are not well known, particularly among animals in top trophic levels like large carnivores. Furthermore, we currently lack understanding of how the impacts of climate variability on individual carnivore behaviour are linked to intraguild dynamics, in part because multi‐species datasets collected at timescales relevant to climatic changes are rare.Using 11 years of GPS data from four sympatric large carnivore species in southern Africa—lions (Panthera leo), leopards (Panthera pardus), African wild dogs (Lycaon pictus) and cheetahs (Acinonyx jubatus)—spanning 4 severe drought events, we test whether drought conditions impact (1) large carnivore space use, (2) broad‐scale intraguild spatial overlap and (3) fine‐scale intraguild interactions.Drought conditions expanded space use across species, with carnivores increasing their monthly home range sizes by 35% (wild dogs) to 66% (leopards). Drought conditions increased the amount of spatial overlap between lions and subordinate felids (cheetahs and leopards) by up to 119%, but only lion‐cheetah encounter rates were affected by these changes, declining in response to drought.Our findings reveal that drought has a clear signature on the space use of multiple sympatric large carnivore species, which can alter spatiotemporal partitioning between competing species. Our study thereby illuminates the links between environmental change, animal behaviour and intraguild dynamics. While fine‐scale avoidance strategies may facilitate intraguild coexistence during periodic droughts, large carnivore conservation may require considerable expansion of protected areas or revised human‐carnivore coexistence strategies to accommodate the likely long‐term increased space demands of large carnivores under projected increases in drought intensity. 
    more » « less