Carlos Chavez Ramirez
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carloschalicothere.bsky.social
Carlos Chavez Ramirez
@carloschalicothere.bsky.social
61 followers 53 following 73 posts
Synthetic Biology, Molecular Genetics, Science Communication

Cell-Free SynBio PhD @ UF
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carloschalicothere.bsky.social
"#RIP Domestic dog 🐕 A GWAS of 6,000 dogs, the first consumer genomics study in any non-human species, found a 98.6kb DNA duplication near eye development gene ALX4 that explains the famous blue eyes of Siberian Huskies. One tiny copy change! #2026MMM #RIP
journals.plos.org/plosgenetics...
"Fig 1. A) Manhattan plot of associations with blue vs. brown eyes across the genomes of 3,180 dogs. Horizontal lines represent the thresholds for suggestive (grey; P < 1x10-5) and significant (black; P < 5x10-8) associations. B) Read depth (scaled by the average depth across the interval for each dog) in 10-kb sliding windows across the CFA18 GWAS peak region, for the six Siberian Huskies with publicly available whole genome sequence data (blue) and 11 dogs from other breeds (grey). Five of the six huskies and five of the 11 other breeds carry the GWAS allele associated with blue eyes (dot at 44,924,848). Black vertical lines indicate paired-end reads that aligned 98.6-kb from their mate and in an opposite orientation. Photo credit: Aleksey Gnilenkov"
March 20, 2026 at 2:11 AM
carloschalicothere.bsky.social
A new cat coat color (“salmiak,” or salty licorice - yum!) isn’t due to a mutation in the gene KIT, but to a deletion of DNA next to it.
Cats with this white hair pattern are missing ~95,000 bases .... maybe removing regulatory DNA that controls how KIT is used. #2026MMM doi.org/10.1111/age....
"Salmiak coat coloration in cats. Hallmarks include tuxedo (bicolor) white spotting despite absence of known white spotting alleles (Ws, g), and pigment dilution within individual hairs, producing pale or unpigmented tips across the body, legs, and tail. Additional features include colored spotting within white areas of the forelegs and chest, intensified pigmentation over the scapular region, and a very pale tail tip. (a) Solid black; (b) solid blue; (c) brown mackerel tabby with heterozygous sibling; (d) long-haired solid black; (e) solid black; (f) tortoiseshell"
March 20, 2026 at 2:01 AM
carloschalicothere.bsky.social
Is your golden retriever friendly because of its breed? Genetics says: not really. A citizen science study of 18,000+ dogs found breed explains only 9% of behavioral variation in individual dogs. Personality predates modern breeds by thousands of years. #2026MMM www.science.org/doi/10.1126/...
"Effect of breed on behavior. (A) Biddability is among eight behavioral factors defined from surveys. SE, standard error. (B) Dogs in some breeds tend to score unusually high or low for this factor compared with dogs overall. (C and D) Border collies score lower on average for biddability (vertical line at median) but vary widely (C), including genetically confirmed border collies (D). (E) In mixed-breed dogs, border collie ancestry has a small genetic effect on biddability. [Photo credits: K. Wirka (Sprocket); M. Wisniewski (Caboose); B. Hoadley (Molly); M. Logsdon (Hunter); A. Macias (Lily); S. Staples (TWooie)]"
March 20, 2026 at 1:59 AM
carloschalicothere.bsky.social
White Stork keeps its antibiotic resistance genes to itself. No genetic similarity between stork gut bacteria and soil/food microbes—only water shows a strong match, changing the inferred transmission pathway. White stork: a sentinel, not a vector. #2026MMM #RIP doi.org/10.1128/spec...
Correlation matrix showing Spearman rank correlation coefficients between selected functional groups of bacteria isolated from different environments (soil, water, and cloacal samples). The results indicate moderate negative relationships among certain bacterial groups, suggesting limited exchange or overlap in the microbial composition across these habitats.
March 20, 2026 at 1:55 AM
carloschalicothere.bsky.social
Fecal genetics in White Stork reveals widespread antibiotic resistance. Because White Stork likes eating our trash? NO. No strong correlation with landfill feeding. Instead, exposure likely comes from other sources, like livestock pastures #2026MMM doi.org/10.1016/j.sc...
Graphical abstract from Francisco et al 2025
March 20, 2026 at 1:39 AM
carloschalicothere.bsky.social
Canine distemper virus (CDV) is a deadly virus that infects carnivores. Weckworth et al. (2020) revealed that CDV outbreak in the Serengeti was caused by spillover from canids (incl. 🐕) and ultimately caused the lion population in the region to decline by 30%. doi.org/10.1111/mec.... #2026MMM
Phylogenetic tree of canine distemper virus genomes from lions, hyenas, domestic dogs, bat-eared foxes, and hyenas. Colors represent different lion prides. Tree shows putative CDV origin in canids (domestic dogs and bat-eared foxes) spilling over into hyenas and lions.
March 20, 2026 at 1:37 AM
carloschalicothere.bsky.social
Semi-wild orangutans are more likely to be infected with nodular worms than free-ranging orangutans. This may be due to a decreased arboreal lifestyle, more soil contact, changes in diet, and overlapping ranges with other wildlife species and livestock #2026MMM #RIP doi.org/10.1038/s415...
Haplotype network of parasitic nematode haplotypes. The color indicates sampling location with green representing semi-wild populations in Bukit Lawang and blue/red representing free-ranging populations. The size of the circles represents frequency of haplotype, with sequences from semi-wild locations heavily-represented
March 20, 2026 at 1:34 AM
carloschalicothere.bsky.social
Alu elements are DNA pieces that can copy and reinsert themselves. Orangutan genomes only show ~250 recent Alu insertions compared to 1000s in chimps and humans. This may explain why their genome structure is more stable and evolving more slowly than other great apes #2026MMM doi.org/10.1038/natu...
A phylogeny shows the evolutionary relationships among the great apes. The pie charts show total number of mobile genetic element insertions. On the right, insertion rates per million years is shown. Data shows that orangutans have much fewer Alu element insertions compared to humans and chimpanzees.
March 20, 2026 at 1:22 AM
carloschalicothere.bsky.social
Cell lines are a useful genetic resource for species conservation and research. Researchers established cell cultures from skin samples of a hippo for the first time. Karyotypes from these cells showed 36 chromosomes, confirming the origin as a female common hippo. #2026MMM doi.org/10.1002/cbin...
Karyotyping of the established hippo fibroblast cell culture. (a) Karyotyping of the fibroblast cell culture was performed based on the Giemsa staining method. A representative of the cell spreads is shown here. Scale bar = 10 μm.(b) A total of 36 chromosomes were rearranged into 18 pairs, one of which was X chromosomes.
March 20, 2026 at 1:20 AM
carloschalicothere.bsky.social
Giraffe was thwarted this round and in fact, some geographic features may thwart interbreeding between giraffe (sub)species. Genome sequences from 78 giraffes from 13 countries in Africa suggest the Central African rainforest may be a key barrier #2026MMM #RIP doi.org/10.1016/j.cub.2024.02.051
(A) Genetic differentiation between giraffe subspecies (values correspond to pairwise Hudson FST estimates derived from the site frequency spectrum). (B) Estimating Effective Migration Surfaces (EEMS) plot of migration rates (log(m); colored brown [low gene flow] to blue [high gene flow]) between locations of sampled giraffes throughout Africa. Colors of dots correspond to (sub)species colored in (A). (C) EEMS plot of migration rates in east Africa (black box in (B)).
March 20, 2026 at 1:16 AM
carloschalicothere.bsky.social
Giraffes have long necks and a long history of scientists debating their taxonomy! 1 species with 9 subspecies had generally been accepted, but whole genome data from 50 giraffes from all previously recognized subspecies support 4 species and 7 subspecies! #2026MMM doi.org/10.1016/j.cub.2021.04.033
Overview of Admixture results based on genome-wide SNPs supporting four giraffe species (top)—northern giraffe (Giraffa camelopardalis), the reticulated giraffe (G. reticulata), the Masai giraffe (G. tippelskirchi), and the southern giraffe (G. giraffa)—and 7 subspecies (bottom). Colors correspond to (sub)species membership. Map of sub-Saharan Africa shows the geographic ranges of each giraffe (sub)species where colors correspond to (sub)species colors from Admixture results.
March 20, 2026 at 1:06 AM
carloschalicothere.bsky.social
Genome analysis of 8 rhino species (extinct & living) show an overall decline in pop size in the past 2 million years. Although this low genetic diversity may be a long-term feature of the rhino family, it has likely been worsened by recent human-driven pop declines #2026MMM doi.org/10.1016/j.ce...
A graph showing time since the present on the x-axis and effective population size in the y-axis. Each curve represents one species. Species are grouped by geographic distribution: Africa, black and white rhinoceroses; South Asia, Sumatran, Javan, and greater one-horned rhinoceroses; and northern Eurasia, Siberian unicorn, Merck’s, and woolly rhinoceroses.
March 20, 2026 at 1:05 AM
carloschalicothere.bsky.social
Across 57 Arabian Oryx samples, only three MHC (gene involved in infectious disease resistance) alleles were observed. However, the 3 alleles are highly different from each other, which may help the oryx population recognize many different pathogens #2026MMM #RIP doi.org/10.1111/j.00...
A graph showing heterozygosity at each amino acid position in the Arabian Oryx MHC gene. The positions marked with asterisks are antigen binding sites. The highest heterozygosity is observed at these sites, which may help the population recognize a wide array of pathogens even though there are few alleles.
March 20, 2026 at 12:56 AM
carloschalicothere.bsky.social
After a herd of Arabian oryx suffered an outbreak from an unknown agent, Coronavirus (CoV) particles were found in sick individuals. CoV particles were present in several tissues, including intestines and heart. This work could help treat infected herds. #2026MMM doi.org/10.1128/spec...
(A) RT-qPCR results confirming the presence of coronavirus in tissue samples from a sick Arabian oryx. (B-I) Immunohistochemistry staining using anti-nucleocapsid antibodies in different tissue samples from a sick animal. Strong positive signals are indicated by black arrows
March 20, 2026 at 12:49 AM
carloschalicothere.bsky.social
Around 50,000 Asian elephants remain in the wild and are scattered across South/South-East Asia in isolated populations. Whole genome data confirms 4 subspecies—Bornean, Sumatran, Mainland, and Sri Lankan—and suggests they began diverging 169,000-48,000 yrs ago. #2026MMM doi.org/10.1002/ece3.72019
Asian elephant populations included in this study (colored by their IUCN subspecies designation and confirmed with whole genome data).
March 20, 2026 at 12:47 AM
carloschalicothere.bsky.social
Gorilla is gone and so is the “ghost” lineage that left its mark on 3% of eastern gorilla DNA! This archaic group split >3 mya from the ancestor of living gorillas. It has not been sampled directly--it was only detected via its DNA in eastern gorillas #2026MMM #RIP doi.org/10.1038/s41559-023-02145-2
Model of gorilla population history over more than 3 million years in the past. A model including archaic admixture from a “ghost” lineage into the common ancestor of eastern gorillas (mountain + eastern lowland gorillas) best explains the empirical data. Numbers on teal blocks correspond to inferred effective population sizes.
March 20, 2026 at 12:45 AM
carloschalicothere.bsky.social
In the last century, Grauer’s+mountain (⛰) gorillas (🦍) ⬇️ but ⛰🦍 now show signs of some recovery. 🦍 genomes today have ⬇️diversity, ⬆️inbreeding, + ⬆️costly mutations vs 100 yr old samples only in Grauer’s (not ⛰) 🦍, maybe b/c of ⛰🦍 recovery + longer-term past #2026MMM doi.org/10.1016/j.cub.2018.11.055
(A) Heterozygosity of gorilla individuals genome-wide (solid outlined boxplots) and outside runs of homozygosity (ROH [inbred regions]; dotted outlined boxplots). Each black dot corresponds to one gorilla individual. ** = p < 0.01; NS = not significant. Pink corresponds to modern western lowland gorillas; orange and yellow correspond to historic and modern Grauer’s (eastern lowland) gorillas, respectively; dark grey and light grey correspond to historic and modern mountain gorillas, respectively. (B) Proportion of gorilla genomes in ROH >100 kb (open bars), and long ROH 2.5-10 Mb (solid bars). Error bars = ±1 SD; * = p < 0.05, ** = p < 0.01; NS = not significant. Colors as in (A).
March 20, 2026 at 12:32 AM
carloschalicothere.bsky.social
Humpback whales (+ many other whales) have evolved large body sizes + long lives. Cancer should ⬆️ w/body size + age but whales do not suffer ⬆️ cancer risk. 212 genes in the humpback whale genome show evidence of positive selection, some of which may ⬇️ cancer #2026MMM doi.org/10.1093/molbev/msz099
(A) Species tree relationships of six cetaceans with genome assemblies, including the humpback whale. Branch lengths are in coalescent units. Boxed numbers correspond to the number of positively selected genes per branch. (B) Gene Ontology (GO) biological process terms for positively selected genes across all cetaceans. (C) Cancer gene names and functions from the COSMIC database that are under positive selection in cetaceans. Superscripts next to gene names correspond to tumor suppressor gene (T), oncogene (O), and fusion gene (F) and asterisks correspond to FDR corrected p-value < 0.01 (**), 0.001 (***), 0.0001 (****).
March 20, 2026 at 12:30 AM
carloschalicothere.bsky.social
#RIP Eurasian Eagle Owl 🦉 Owl feathers have comb-like serrated edges and a velvety surface that muffle air turbulence for near-silent flight. Nocturnal owls like Bubo bubo have more serrations than day-active owls of similar size. Super stealth! #2026MMM doi.org/10.1371/jour...
"Fig 9. Serrated structures on owl wings. The serrations of all 7 investigated owl species are presented for 4 different measurement positions. Note the variation in shape between the different species and between the different positions within one species. The black bars represent 1 mm. https://doi.org/10.1371/journal.pone.0149236.g009"
March 20, 2026 at 12:27 AM
carloschalicothere.bsky.social
Eastern & western grey fox populations split ~800,000 years ago, making them more genetically distinct than most animal species that share a name. DNA from 378 foxes pinpoints where these ancient lineages still meet today: the Great Plains! #2026MMM doi.org/10.3389/fevo...
Analysis of 400 bp mtDNA control region sequence data from samples of gray fox (Urocyon spp.). (A) Map shows the ranges of 7 morphologically-based gray fox (U. cinereoargenteus) subspecies (Hall, 1981) and the island fox (U. littoralis); the locations of sample groups (n = 34) and samples (n = 781) used in the analysis, including newly generated sequences (circles), and previously published sequences (squares; Bozarth et al., 2011; Goddard et al., 2015; Hofman et al., 2015); and 3 possible locations of a hypothesized secondary contact zone between deeply divergent eastern and western gray fox lineages (Goddard et al., 2015). Samples are colored according to whether its haplotype fell into the East (white) or West (black) clade. (B) Median joining haplotype network. Each circle represents a unique haplotype, with size proportional to frequency, as well as a pie chart with color indicating the morphologically-based taxonomic assignment of the corresponding samples. Black circles reflect inferred haplotypes not present in the dataset, and hash marks on the lines connecting haplotypes represent the number of mutations separating them. A minimum of 13 steps separates East and West haplotypes. (C) Principal coordinates plot from population pairwise Fst (K2P-corrected) values, with sample groups colored according to morphologically-based taxa shown in the map. The first axis explained 47.8% of the variation and clearly divided western from eastern sample groups at the Great Plains, the second axis explained 11.3% of the variation and separated sample groups within the East (note only scores for East sample groups are shown since West sample groups had scores near 0 for the second axis), and the third axis explained 7.9% of the variation and separated sample groups within the West (note only scores for West sample groups are shown since East sample groups had scores near 0 for the third axis).
March 20, 2026 at 12:18 AM
carloschalicothere.bsky.social
Owls are the only nocturnal raptors. A genome-wide scan across 11 owl species found positive selection on vision genes (e.g. dim-light detection) AND hearing genes (e.g. inner ear development) at the very origin of owls. Their DNA evolved to rule the night! #2026MMM academic.oup.com/gbe/article/...
Fig. 3.Functional overrepresentation of GO terms and KEGG pathways among the genes with a signal of weak positive or relaxed purifying selection (list ii). The GO terms were clustered in seven groups by the ClueGO software (shown in different colors). Each group can contain several GO terms with shared genes. The groups “plasma membrane bounded cell projection” (salmon) and “sensory perception” (purple) form the main part of the network with 87 genes. This main part also overlaps in several genes with the groups “sensory perception of sound” (blue), “transmembrane transporter complex” (gold), “myosin complex” (turquoise), and “supramolecular fiber” (lime). The functional group “DNA conformation change” with 13 genes forms another, more isolated cluster.
March 20, 2026 at 12:16 AM
carloschalicothere.bsky.social
Small but mighty survivors. House mice followed humans into Andes & survived even at high altitudes. Genomic data reveals a threshold effect: hypoxia-related genes show dramatic allele frequency changes in mice living @ highest elevations (~3800m/11,176 stoats) doi.org/10.1093/gene... #2026MMM #RIP
Population allele frequency of autosomal candidate SNPs by elevation. Individual SNPs (gray) and linear regression with all candidates (black) across elevation. (A) Northern transect LFMM candidates with q = 0.05. (B) Southern transect LFMM candidates with q = 0.05. (C) Northern transect, SNPs from top 1 % of PBSn1 results. (D) Southern transect, SNPs from top 1 % of PBSn1 results. SNPs with large allele frequency change (LAFC) from below to above ∼2900 m in red.
March 20, 2026 at 12:13 AM
carloschalicothere.bsky.social
Dogs aren't the only ones who evolved to eat your leftovers. House mice, rats & pigs have MANY extra copies of the amylase gene that helps digest starch. Big clue about who has been eating our table scraps for 1000s of years. doi.org/10.7554/eLif... bsky.app/profile/cega... #2026MMM
"Amylase gene copy number bursts across mammals. Boxes represent all haploid amylase gene copies found in representative species or among clades across the mammalian phylogeny. Lighter colored boxes represent the variation in copy numbers found in at least two individuals of a given species or in reference genomes of at least two species within a clade. Triangles at the end of branches indicate that copy numbers of more than one species belonging to the same clade were shown together as a single column. The numbers in parentheses following clade names indicate the number of species used for estimating the gene copy numbers."
March 20, 2026 at 12:07 AM
carloschalicothere.bsky.social
Kasai et al. (2012) used chromosome painting to show extensive homology (70%!) between Nile Crocodile (2n = 32) & chicken (2n = 78) chromosomes (focusing on larger chromosomes) despite a common ancestor 230 MYA! doi.org/10.1159/0003... #2026MMM
"The phylogenic tree between G. g. domesticus , T. s. elegans and C. niloticus is based on 2 hypotheses; a branch point leading to crocodile lineage is different between morphological (A) and molecular (B) studies. Idiograms show chromosome homology of GGA1–8 and Z with TSC and CNI chromosomes revealed by cross-species chromosome painting. Homologous regions are identified by colour. The uncoloured regions, TSC4p and 8p have no homology to GGA1–8 and Z. Fissions of ancestral metacentric chromosomes have occurred during crocodile evolution, resulting in the formation of metacentric chromosomes with other acrocentric chromosomes by fusion. "
March 20, 2026 at 12:05 AM
carloschalicothere.bsky.social
Spectacled bear didn’t win but don’t worry, it will not be forgotten! Spectacled bears are unique in many ways relative to their bear cousins, incl. having 52 chromosomes vs. 74 in the American/Asian black bear, sun bear, sloth bear, brown bear, & polar bear! #2026MMM #RIP doi.org/10.1159/000132455
Comparison of spectacled bear chromosomes (left chromosome in each pair and number below each pair) vs. brown bear chromosomes (right chromosome in each pair and numbers to the right of each pair).
March 12, 2026 at 2:02 AM