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1. Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents

   https://doi.org/10.1002/ece3.6138  

   French, Beverly J. ; Lim, Yan Wei ; Zgliczynski, Brian J. ; Edwards, Robert A. ; Rohwer, Forest ; Sandin, Stuart A. ( March 2020 , Ecology and Evolution)

   Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genusParacirrhitesare a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo–Malay–Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next‐generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence.

   Flint Island, Southern Line Islands, Republic of Kiribati.

   A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four “arc‐eye” hawkfish species in theParacirrhitesspecies complex and a potential hybrid. Fish from fourParacirrhitesspecies were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species.

   Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering ofP. bicolorwithP. arcatusandP. xanthuswithP. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches.

   Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus,P. xanthus, andP. bicolor) cluster separately from the more broadly distributedP. arcatuson the basis of relative abundance of metazoan sequences in the gut (presumed prey remains).Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.

    

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2. Differential geographical and ecological dynamics allow diversification of morphologically convergent giant bromeliads in the Atlantic Forest

   https://doi.org/10.1111/jbi.13961  

   Maciel, Jefferson Rodrigues ; Zizka, Georg ; Alves, Marccus ( October 2020 , Journal of Biogeography)

   We investigate the evolutionary mechanisms that allow morphologically convergent lineages to share the same geographical space. We compared the evolutionary events that occurred along the diversification ofKarawataandAechmeasubgen.Chevalierain the Atlantic Forest by (a) verifying whether the climatic niches and habitats ofKarawataandChevalieraare similar; (b) testing whether the two groups had the same pattern of colonization in the Atlantic Forest; and (c) evaluating whether they had the same evolutionary dynamics of environmental space occupation.

   Brazilian Atlantic Forest

   KarawataandAechmeasubgen.Chevaliera(Bromeliaceae: Bromelioideae)

   We explored differences in evolutionary dynamics betweenKarawataandChevalieraby (a) analyzing their divergence times using Bayesian inference with a relaxed molecular clock; (b) estimating ancestral ranges and habitats with Dispersion Extinction Cladogenesis Lagrange and Statistical Dispersal Vicariance analyses; (c) testing climatic niche similarity, equivalency and overlap using principal component analysis; and, (d) evaluating shifts in speciation dynamics using Bayesian Analysis of Macroevolutionary Mixtures.

   KarawataandChevalieramost likely originated in the Pliocene and diversified during the Pleistocene. The two clades originated in ombrophilous forests and shared a similar environmental space. However,KarawataandChevalierashow different dynamics in the occupation of geographical and environmental spaces.

   Our results suggest that the São Francisco and Jequitinhonha Rivers acted as geographical barriers forKarawataandChevaliera. Differences in spatial and environmental evolutionary dynamics have allowed the two groups to occupy similar habitats as well as environmental and geographical spaces in the Brazilian Atlantic Forest.

    

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3. The influence of history, geography and environment on patterns of diversification in the western terrestrial garter snake

   https://doi.org/10.1111/jbi.14146  

   Hallas, Joshua M. ; Parchman, Thomas L. ; Feldman, Chris R. ( June 2021 , Journal of Biogeography)

   A central aim of biogeography is to understand how biodiversity is generated and maintained across landscapes. Here, we establish phylogenetic and population genetic patterns in a widespread reptile to quantify the influence of historical biogeography and current environmental variation on patterns of genetic diversity.

   Western North America.

   Western terrestrial garter snake,Thamnophis elegans.

   We used double‐digest RADseq to estimate phylogenetic relationships and characterize population genetic structure across the three widespread subspecies ofT. elegans:T. e. vagrans(wandering garter snake),T. e. elegans(mountain garter snake) andT. e. terrestris(coast garter snake). We assessed patterns of dispersal and vicariance across biogeographic regions using ancestral area reconstruction (AAR) and deviations from isolation‐by‐distance across the landscape using estimated effective migration surfaces (EEMS). We identified environmental variables potentially shaping local adaptation in regional lineages using genetic‐environment association (GEA) analyses.

   We recovered three well‐differentiated genetic groups that correspond to the three subspecies. AAR analyses inferred the eastern Cascade Range as the ancestral area, with dispersal to both the east and west across western North America. Populations ofT. e. elegansdisplayed a latitudinal gradient in genetic variation across the Sierra Nevada and northern California, while populations ofT. e. terrestrisshow discrete genetic breaks consistent with well‐known biogeographic barriers. Lastly, GEA analyses identified allele frequency shifts at loci associated with a common set of environmental variables in bothT. e. elegansandT. e. terrestris.

   T. elegansis composed of distinct evolutionary lineages, each with its own geographic range and history of diversification.T. e. elegansandT. e. terrestrisshow unique patterns of diversification as populations dispersed from east to west and while adapting to the new environments they colonized. Historical events, landscape features and environmental variation have all contributed to patterns of differentiation inT. elegans.

    

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4. Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world’s largest bats (Mammalia: Chiroptera)

   https://doi.org/10.1111/jbi.13750  

   Tsang, Susan M. ; Wiantoro, Sigit ; Veluz, Maria Josefa ; Sugita, Norimasa ; Nguyen, Y‐Lan ; Simmons, Nancy B. ; Lohman, David J. ( November 2019 , Journal of Biogeography)

   Islands provide opportunities for isolation and speciation. Many landmasses in the Indo‐Australian Archipelago (IAA) are oceanic islands, and founder‐event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group.

   Australasia, Indo‐Australian Archipelago, Madagascar, Pacific Islands.

   Pteropus(Pteropodidae).

   To infer the biogeographic history ofPteropus, we sequenced up to 6,169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognizedPteropusspecies and subspecies with threeAcerodonoutgroups usingBEASTand subsequently estimated ancestral areas using models implemented inBioGeoBEARS.

   Species‐level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor withAcerodon; founder‐event speciation out of Wallacea was a common inference.Pteropusspecies in Micronesia and the western Indian Ocean were also inferred to result from founder‐event speciation.

   Dispersal between regions of the IAA and the islands found therein fostered diversification ofPteropusthroughout the IAA and beyond. Dispersal inPteropusis far higher than in most other volant taxa studied to date, highlighting the importance of inter‐island movement in the biogeographic history of this large clade of large bats.

    

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5. RhoA/ROCK signalling activated by ARHGEF3 promotes muscle weakness via autophagy in dystrophic mdx mice

   https://doi.org/10.1002/jcsm.13278  

   You, Jae‐Sung ; Kim, Yongdeok ; Lee, Soohyun ; Bashir, Rashid ; Chen, Jie ( June 2023 , Journal of Cachexia, Sarcopenia and Muscle)

   Duchenne muscular dystrophy (DMD), caused by dystrophin deficiency, leads to progressive and fatal muscle weakness through yet‐to‐be‐fully deciphered molecular perturbations. Emerging evidence implicates RhoA/Rho‐associated protein kinase (ROCK) signalling in DMD pathology, yet its direct role in DMD muscle function, and related mechanisms, are unknown.

   Three‐dimensionally engineered dystrophin‐deficientmdxskeletal muscles andmdxmice were used to test the role of ROCK in DMD muscle functionin vitroandin situ, respectively. The role of ARHGEF3, one of the RhoA guanine nucleotide exchange factors (GEFs), in RhoA/ROCK signalling and DMD pathology was examined by generatingArhgef3knockoutmdxmice. The role of RhoA/ROCK signalling in mediating the function of ARHGEF3 was determined by evaluating the effects of wild‐type or GEF‐inactive ARHGEF3 overexpression with ROCK inhibitor treatment. To gain more mechanistic insights, autophagy flux and the role of autophagy were assessed in various conditions with chloroquine.

   Inhibition of ROCK with Y‐27632 improved muscle force production in 3D‐engineeredmdxmuscles (+25% from three independent experiments,P < 0.05) and in mice (+25%,P < 0.001). Unlike suggested by previous studies, this improvement was independent of muscle differentiation or quantity and instead related to increased muscle quality. We found that ARHGEF3 was elevated and responsible for RhoA/ROCK activation inmdxmuscles, and that depleting ARHGEF3 inmdxmice restored muscle quality (up to +36%,P < 0.01) and morphology without affecting regeneration. Conversely, overexpressing ARHGEF3 further compromisedmdxmuscle quality (−13% vs. empty vector control,P < 0.01) in GEF activity‐ and ROCK‐dependent manner. Notably, ARHGEF3/ROCK inhibition exerted the effects by rescuing autophagy which is commonly impaired in dystrophic muscles.

   Our findings uncover a new pathological mechanism of muscle weakness in DMD involving the ARHGEF3‐ROCK‐autophagy pathway and the therapeutic potential of targeting ARHGEF3 in DMD.

    

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