Carlos Chavez Ramirez
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carloschalicothere.bsky.social
Carlos Chavez Ramirez
@carloschalicothere.bsky.social
36 followers 51 following 24 posts
Molecular Genetics, Neuroscience, Science Communication
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carloschalicothere.bsky.social
The Maned Wolf (Chrysocyon brachyurus) may look like a fox, but it’s neither a fox nor a wolf! A phylogenetic study using 15K bases of DNA shows it belongs to a distinct group of canids endemic to South America. #2025MMM #RIP www.nature.com/articles/nature04338
Shown is a phylogenetic tree for canids based on ∼15 kb of DNA sequence. Branch colors identify the red-fox-like clade (red), the South American clade (green), the wolf-like clade (blue) and the grey and island fox clade (orange). Underlined species names are represented with corresponding illustrations. The figure features an image of the Maned Wolf (2025 MMM combatant), as well as other canids such as the Arctic fox, red fox, domestic dog, coyote, and the African Painted Dog (2024 MMM combatant).
March 21, 2025 at 1:54 AM
carloschalicothere.bsky.social
Recent genetic work from Dutra et al. using nuclear and mitochondrial markers has shown that the chacoan peccary should be placed in the distinct genus Parachoerus in 2016. Their former genus 'Catagonus' is just a pig-ment of their imagination! #2025MMM link.springer.com/article/10.1...
Phylogenetic tree of new world pigs with former species classification at tips. Single most parsimonious tree from implied weighting analysis with Relative Bremer Supports (RBS) on each node (Right) and Bayesian inference with posterior probability on each node (Left)
March 21, 2025 at 1:47 AM
carloschalicothere.bsky.social
The Maned Wolf (C. brachyurus) has the longest legs of any canid! But what genes drive this extreme phenotype? A genomic study of it & its short-limbed cousin, the bush dog, found that B4GALT7 may play a key role in their striking limb length differences. #2025MMM www.pnas.org/doi/10.1073/...
The figure displays the proportion of private genetic variants in the bush dog (top, green) and the maned wolf (bottom, blue). Identifying private variants in species with divergent traits can help uncover the genetic basis of their differences. The X-axis represents chromosomes, while the Y-axis indicates the number of private alleles. Genes associated with limb elongation are highlighted with red rectangles.
March 21, 2025 at 1:46 AM
carloschalicothere.bsky.social
And if you thought that Quokkas only had trypanosome parasites, think again -- a novel gammaherpesvirus (MaHV-6) was detected by PCR in the blood of 13 of 121 individuals (11%) sampled in Western Australia. Check out all that viral diversity! #2025MMM #RIP dx.doi.org/10.1638/2020...
"Molecular phylogenetic analysis of MaHV-6. The tree (drawn to scale) with the highest log likelihood (2,672.3425) is shown. The percentage of trees in which the associated taxa clustered together is shown above the branches, with branch lengths measured in the number of substitutions per site. The analysis involved 41 amino acid sequences. There was a total of 52 positions in the final dataset. Herpesviridae subfamilies are indicated to the right of the alignment: Gammaherpesvirinae (c), Betaherpesvirinae (b), and Alphaherpesvirinae (a)."
March 21, 2025 at 1:40 AM
carloschalicothere.bsky.social
Quokkas (Setonix brachyurus) are cute and all (smiley, etc) -- but did you know they have some parasitic friends? Trypanosomes are the unicellular flagellate protozoa that live in their bloodstream and steal nutrients from Quokka. Who's smiling now!? #2025MMM www.sciencedirect.com/science/arti...
The quokka, Setonix brachyurus, is a vulnerable, small marsupial endemic to Western Australia. Blood samples were collected from quokkas from three different geographical locations; Phylogenetic analysis conducted on 47 18S PCR positives identified two Trypanosoma copemani genotypes, with T. copemani genotype B, the most prevalent genotype infecting quokka populations from the three locations with an overall prevalence of 51.8% (24/47) compared to 34% for T. copemani genotype A (16/47). Further work is required to determine the clinical impact of T. copemani on marsupial populations.
March 21, 2025 at 1:29 AM
carloschalicothere.bsky.social
If it ain't broke, don't fix it! Studies using chromosome painting techniques have shown that all members of the family Felidae (including the puma) have 19 pairs of chromosomes (Wie et al. 2011), despite evolving at least 35 million years ago. #2025MMM www.nature.com/articles/hdy...
Phylogenetic tree (depiction of evolutionary relationships of species) showing the 2N (diploid) karyotype numbers across feliforma and caniforma. Notably, the felids (Felidae) all have 2N = 38. Various fission and fusions (breaking apart and fusing of carnivores are annotated.
March 21, 2025 at 1:28 AM
carloschalicothere.bsky.social
Climate change threatens coastal species. Genomic analysis of two horseshoe crabs reveals that the less mobile Carcinoscorpius rotundicauda is losing genetic diversity faster than Tachypleus gigas, making it more vulnerable. Conservation efforts are needed. #2025MMM #RIP doi.org/10.1111/eva....
Genetic differentiation of two horseshoe crab species across the Singapore Straits. Sampling localities are illustrated as circles whose gray scale corresponds to locality-specific F coefficients (calculated based on datasets C0 and T0). PCA plots are re-scaled according to PC values, with the color of sample points adjusted to the color gradient on map. (a) C. rotundicauda; (b) T. gigas. Mangrove distribution by Giri et al. (2011) is illustrated as dark-shaded coastal areas
March 21, 2025 at 1:23 AM
carloschalicothere.bsky.social
Gars have a GC-compartmentalized genome, resembling mammals rather than other fish. This challenges the idea that GC heterogeneity arose with amniotes. Their metabolism may have driven DNA thermostability and genome evolution, supporting the metabolic rate hypothesis #2025MMM doi.org/10.1002/jez....
A time-scaled tree of Osteichthyes highlights genomic and ecophysiological shifts, including whole genome duplications, base compartmentalization, air breathing, and terrestrialization. Gars uniquely show GC compartmentalization among actinopterygians. GC heterogeneity may have arisen multiple times in amniotes or been lost in some reptiles.
March 21, 2025 at 1:17 AM
carloschalicothere.bsky.social
The genome of Limulus polyphemus reveals 18 opsins, shedding light on chelicerate vision & opsin evolution. Phylogenetic analyses highlight key genomic events shaping its visual system, enhancing understanding of horseshoe crab photosensitivity & arthropod evolution #2025MMM doi.org/10.1093/gbe/...
A schematic and phylogenetic tree of Limulus opsins show their distribution across eyes and the nervous system. Opsin transcripts were detected in various tissues, including the brain and tail, with some linked to known photosensitive cells. This highlights the diverse roles of opsins in Limulus vision and neural function.
March 21, 2025 at 1:15 AM
carloschalicothere.bsky.social
Since you won't be seeing any more of our friend the Spotted-necked Otter, here is a last look at more of his furry family -- the Otters of the World! Poster available for the low price of $8.99, can't say that's a bad deal (credit: Roger Hall)
#2025MMM #RIP inkart.net/product/otte...
There are thirteen species of otter in existence today. They’re found various environments on every continent (except Antarctica and Australia.) The poster print features a fine art illustration of all species of otter or Lutrinae including of the world’s most endangered wildlife.
March 21, 2025 at 1:10 AM
carloschalicothere.bsky.social
"The Spotted-necked Otter (Hydrictis maculicollis) used to be called ""Lutra maculicollis"" in case you got confused -- they are handsome devils and have 2n=40 chromosomes, making them only otter species with >38 chromosomes!
#2025MMM doi.org/10.1644/0.71... www.mammaldiversity.org/taxon/100584...
Handsome otter peering from the water (Photo courtesy of Michael Somers) and their distribution across Africa
March 21, 2025 at 12:58 AM
carloschalicothere.bsky.social
Addax is at risk of extinction, w/ <300 individuals in the wild. Armstrong et al. (2010) studied a captive Addax population at the Parque Lecocq Zoo & found low genetic diversity & high inbreeding—a risk for conservation! #2025MMM doi.org/10.1002/zoo.20341
Graph showing changes in the inbreeding coefficient (F, squares) and average relatedness (AR, triangles) in a captive Addax nasomaculatus population over time. Both measures increased steeply at first, with F rising sharply around 1986 and again around 1998, followed by more stable values in recent years (2001-2007). Source: Armstrong et al. (2010) “Genetic structure analysis of a highly inbred captive population of the African antelope Addax nasomaculatus. Conservation and management implications".
March 21, 2025 at 12:57 AM
carloschalicothere.bsky.social
Coelacanths have a unique adaptive immune system, w distinctive IgW loci, no IgM, & tetrapod-like immune genes. Their T-cell receptor organization mirrors tetrapods, raising questions about immune evolution and expanding our understanding of vertebrate immunity. #RIP #2025MMM doi.org/10.1002/jez....
A Maximum Likelihood phylogenetic tree of CD3 proteins was constructed using 30 predicted amino acid sequences across vertebrates. The analysis, based on 234 aligned positions, reveals evolutionary relationships among CD3 subunits (γ, δ, ϵ, ζ), highlighting lineage-specific divergence and conservation in immune signaling.
March 21, 2025 at 12:50 AM
carloschalicothere.bsky.social
Ringed seals populations disperse all across the Arctic and may migrate long distances during the summer months. Martinez-Bakker et al 2014 found that the Lake Saimaa seals do not exchange many seals with other arctic populations and are genetically differentiated doi.org/10.1371/jour... #2025MMM
An estimate of the amount of genetic differentiation between ringed seal breeding sites using pairwise fixation indices (FST). FST for Saimaa pairwise with the Baltic and the nine Arctic breeding sites ranged from 0.30–0.37, where FST values >0.25 are generally taken to represent pronounced levels of genetic differentiation.
March 21, 2025 at 12:42 AM
carloschalicothere.bsky.social
The "living fossil" coelacanth has a 2.74 Gbp genome w 60% repetitive elements and low gen. diversity. It shares tetrapod-like olfactory genes and limb enhancers, hinting at early adaptations in Sarcopterygii and giving insights into fish-tetrapod transition. #2025MMM www.genome.org/cgi/doi/10.1...
A genome comparison across vertebrates reveals genetic signatures of the fin-to-limb transition. Coelacanths retain key limb-associated enhancers (bmp7, gli3, grem1-fmn1), highlighting conserved regulatory elements. Alignment analyses show evolutionary shifts in limb development genes, shedding light on tetrapod origins.
March 21, 2025 at 12:40 AM
carloschalicothere.bsky.social
The most complex and rearranged vertebrate mitochondrial genome is found in the tuatara! Macey et al 2021 find all 37 common vertebrate genes with an extra three control region blocks, and duplicate tRNAs. The tuatara mt-genome shows drastic gene rearrangements #RIP #2025MMM doi.org/10.1038/s420...
Mitochondrial genome gene arrangements depicted as a linear bar for what is a circular molecule. A The standard vertebrate mt-gene order presumptive as ancestral among vertebrates. B The mt-gene order discovered in complete mt-genomes of the Tuatara showing extra NC blocks and duplicated tRNAs. C The standard vertebrate mt-gene order as in “A” above.
March 21, 2025 at 12:35 AM
carloschalicothere.bsky.social
Roots and Relicts can help us understand the evolution of the skin. In vertebrates, this is controlled by the epidermal differentiation complex (EDC). Holthaus, et al 2020 identified EDC genes the tuatara and found them to be close to the snakes and lizards doi.org/10.1038/s415... #2025MMM
Organization of the epidermal differentiation complex (EDC) in the tuatara. Genes of the EDC locus of the tuatara (Sphenodon punctatus) are compared to those of the Japanese gecko (Gekko japonicus), anole lizard (Anolis carolinensis), chicken (Gallus gallus), turtle (Chrysemys picta bellii) and humans. Genes are displayed by arrows pointing in the direction of transcription. Rectangular boxes indicate clusters of similar genes with numbers of genes (#) in these cluster being shown above the boxes. Orthologies of genes and gene families in different species are indicated by vertical lines.
March 21, 2025 at 12:30 AM
carloschalicothere.bsky.social
🦈 Unlike most live-bearing animals, frilled sharks still keep egg yolk genes (VTG). A 2023 study found their genome actively retains these genes, helping sustain embryos for 3.5 years before birth (!!!). Evolution repurposes, rather than erases! #2025MMM doi.org/10.1093/gbe/...
"Cross-species comparison of VTG and VLDLR gene repertoires in Chondrichthyes. The colored box number on the right shows the number of orthologs identified in their genomes or transcriptome assemblies for individual species. Question marks indicate possible orthologs that could not be identified but are inferred only with transcriptome data and remain to be confirmed with whole genome sequencing. The reproductive mode of each species is shown to the right of the species name."
March 21, 2025 at 12:27 AM
carloschalicothere.bsky.social
Forest tortoises determine whether they are born male of female based on the temperature of egg instead of relying on a genetic mechanism. Emer 2007 hatched male tortoises at low temperatures (24.99°C, 27.18°C) and female tortoises at high temperatures (30.79°C) doi.org/10.57709/105... #2025MMM #RIP
Relation between hatching duration of male forest tortoises and sex. Early hatching individuals from warmer nests were all female, wheras all later hatching individuals were all male
March 21, 2025 at 12:24 AM
carloschalicothere.bsky.social
The forest tortoise may be a Root and Relict but it's not alone! Le et al 2006 use mitochondrial and nuclear genes and found the most basal testudinid lineage is a novel sister relationship between the Asian forest tortoises and the North American gopher tortoises doi.org/10.1016/j.ym... #2025MMM
Phylogeny of the testudines based on five genes. The Manouria from East Asia along with Gopherus from North America are the most basal clade in the family. Species to the outside of this clade are outgroups from outside the testudines for comparison.
March 21, 2025 at 12:18 AM
carloschalicothere.bsky.social
Species-specific genome databases allow us to better study the evolution and conservation status of Roots and Relicts. Gu et al 2022 created GinkgoDB, the ecological genome database for the world-renowned living fossil, Ginkgo biloba; containing 545 ginkgo genomes doi.org/10.1093/data... #2025MMM
GingkoDB includes four sets of data: genome data, geographic location data, monitoring data of both species and habitats from 27 plots of natural ginkgo forests, field morphological photos and scanned phenotypic images of various ginkgo materials.
March 21, 2025 at 12:17 AM
carloschalicothere.bsky.social
Madagascar's giant lemurs may be gone, but their DNA tells a story! An ancient DNA study found that extinct giant lemurs were closely related to Indriidae—the family of living indris. #2025MMM #RIP link.springer.com/article/10.1...
Model for the evolution indrioids from Orlando et al. (2008). The model places Archaeolemurids as an outgroup for both Indriids and Palaeopropithecids, and indicate in which lineage traits such as increased forelimb activities, accelerated dental development, and postcranial specializations for increased ground locomotion have arisen.
March 21, 2025 at 12:13 AM
carloschalicothere.bsky.social
What colors can Indri see? A study of opsin genes found that they have more genetic variation than other lemurs, w/ at least 3 variants influencing color vision. This variation could potentially help Indris distinguish ripe fruits more effectively. #2025MMM royalsocietypublishing.org/doi/10.1098/...
A phylogenetic tree of 11 lemur species, including Indri indri, displaying amino acid variants at three key functional sites (180, 277, and 285) in the opsin gene. A table to the right provides data for each species, including body size, activity cycle, genetic polymorphism at these sites, estimated spectral sensitivities, and sample sizes. I. indri is a highly diurnal species, weighing ~6–9 kg, and exhibits the greatest number of genetic variants among the sampled lemurs.
March 21, 2025 at 12:07 AM
carloschalicothere.bsky.social
Saiga antelope (Saiga tatarica) used to be WAY more widespread. Prior to 10,000 years ago, their range spanned from France to the NW Territories of Canada -- this lasted until the end of the Soviet Union, after which its populations shrunk by >95% #2025MMM onlinelibrary.wiley.com/doi/abs/10.1...
Geographic origin of modern and ancient samples used in this study (ancient samples in red and modern samples in green). Dashed line represents the area where the species is known to have existed during historical times (17th–18th century).
March 21, 2025 at 12:06 AM