Anne Stone

@acstone.bsky.social

1246 Followers 741 Following

Professor, anthropological geneticist, gardener, mom of 1. I dabble in stained glass, embroidery, and print making in my copious free time. Opinions my own

A roadside sign for “guy stuff”

Sewing Susan assorted needles. Susan is sitting in the midst of an enthralled group of ladies who are watching her triumphantly pull a needle through fabric. They all either had way too many martinis or are fervently wishing they were elsewhere.

Skull embroidery on a tea towel.

Tea towel embroidery: a finished Darwin phylogeny and a just started skull that hopefully will actually look like the original etching.

Miriam Bravo, Maria Nieves-Colon, Genevieve Houseman, me, Tanvi Honap and Joanna Malukiewicz

Miriam starting her talk at SMBE! (Sorry for the terrible angle but someone with a big head was sitting in front of me)

At SMBE 2026!

Anne, Miriam and Mario at Stockholm City Hall

Miriam Bravo presenting at ICP2026

Banksy’s Blind patriotism while Athena surrounded by scaffolding looks on…perhaps a reminder that democracy always takes work.

Anne and Maxine holding a funfetti cake that has DNA in sprinkles along with some sad attempts at drawing M. tuberculosis and skeleton in icing. Funfetti is not the cake that Anne typically makes students but 2 of her students (including Maxine) are Funfetti aficionados. Basically, important life events are meant to be celebrated with cake (and bubbles which are not shown in the image).

From the executive summary of the proposed NSF budget for FY27: Directorate for Social, Behavioral, and Economic Sciences. In FY 2027, NSF will close-out this directorate. Continuing grants that align with Administration priorities, such as in behavioral and cognitive science, and all impacted employees will be transferred to other parts of the agency. The National Center for Science and Engineering Statistics will operate independently of the directorates and continue to be supported through the R&RA appropriation.

Chart showing cumulative number of awards from the NSF BIO directorate. Currently = 38 whereas in previous years it was 204-353 by this time of year.

data showing cumulative number of awards from the Social, Behavioral, and Economic directorate at NSF for the past few fiscal years. In FY26, the number to date is 16. In previous years by now over 150 are funded. WRITE YOUR CONGRESS PEOPLE!!!

Directorate for Social, Behavioral, and Economic Sciences. In FY 2027, NSF will close-out this directorate. Continuing grants that align with Administration priorities, such as in behavioral and cognitive science, and all impacted employees will be transferred to other parts of the agency. The National Center for Science and Engineering Statistics will operate independently of the directorates and continue to be supported through the R&RA appropriation.

Admixture plot showing different tiers of lion structure across continent. Each line represents an individual, and each color represents the ancestry likelihood of that individual. Dfiferent rows show results when data is clustered into different numbers of groups.

Sample map (A) and phylogeny (B) of lion lineages. Phylogeny distinguish sourthern and northern lineages with the cave lion as a distant outgroup. Tree is rooted on the leopard (Panthera pardus). Values correspond to bootstraps.

Phylogeographical analysis of South American alligatorid and African crocodilid trypanosomes: Phylogenetic relationships and geographical origin of trypanosomes from South American alligatorids, African crocodilids, and tsetse flies. ML phylogeny based on gGAPDH sequences (810 characters, –Ln = −10359.469307) from the trypanosomes nested into the Crocodilian clade (GenBank accession numbers are on Table 1), and trypanosomes from other hosts (GenBank accession numbers are within parenthesis on the tree). Numbers at nodes are bootstrap support >50% (P/ML) or Bayesian posterior probability > 0.25, derived from 500 replicates.

A statistical parsimony network showing relationships between hippopotamus mtDNA haplotypes from eastern and southern Africa. Haplotypes are represented as circles and squares for ancestral ones. The minimum number of steps connecting parsimoniously two haplotypes is indicated as a thick-black square, and a filled-small circle represents an extinct or missing haplotype that might have not been sampled. The size of the square or circle and pattern assigned correspond to the haplotype frequency and population, respectively, and numbers in haplotypes correspond to the number of individual sharing the haplotypes.

Protein–protein interaction networks for 105 protein-coding gene products tested in both cetaceans and the hippo that were found to be under positive selection in cetaceans. Inset: protein–protein interaction networks for 20 protein-coding genes found to be under positive selection in the hippo. Nodes are labelled with the standard protein names, and the thickness of each connection represents the strength of support. (a) Highlights proteins involved in the circulatory system (red) and (b) highlights proteins involved in muscle (yellow) the nervous system (blue) or both (yellow with blue).

Reconstruction of historical effective population size (Ne) for all baleen whale genomes analyzed (humpback whale is colored in pink). Generation times (g) for each species are listed next to each species’ name. Light brown shading corresponds to interglacial periods (IG) in the Pleistocene and Holocene and gray shading corresponds to the mid-Pleistocene transition (MPT) and the Plio-Pleistocene transition (PPT).

Figure with four panels illustrating the genomics and history of the extinct Steller’s sea cow. (A) Artistic reconstruction of 18th-century sailors from Vitus Bering’s 1741 expedition butchering sea cows on a shoreline. (B) Map of the Bering Sea region showing the species’ former Late Pleistocene range (yellow), archaeological sites with sea cow remains (red circles), and locations of the last known populations (blue circles). (C) Photograph of a pars petrosa of the petrous bone, used for ancient DNA extraction. (D) Graph of effective population size through time for Steller’s sea cow compared to dugong, woolly mammoth, and Lena horse, showing long-term population decline in the sea cow prior to the more recent extinction. Source: Sharko et al. (2021) Nature Communications.

Geographic contour map of the genetic relation of the extinct aurochs genome admixture with European cattle breeds. Irish and English breeds are more admixed with the ancient auroch individual than any other breed in Europe.

Time-calibrated phylogenetic tree of mammals highlighting the Sirenia (blue shaded box), including the extinct Steller’s Sea Cow (Hydrodamalis gigas), dugong (Dugong), and manatees (Trichechus). Divergence times (in millions of years) are shown at key nodes with red circles marking calibrated points. Sirenians cluster with elephants (Loxodonta, Elephas) and hyraxes (Procavia, Heterohyrax) within Afrotheria. Within Sirenia, Hydrodamalis and Dugong form a close lineage (dugongids), separate from manatees. This evolutionary context helps interpret genetic changes such as the loss of enamel-related genes (like ENAM) in the Steller’s Sea Cow and their evolution within Afrotheria.

Gila monsters are one of only two venomous lizard species in the world. They live in the southwestern U.S. and in Mexico. This animated GIF comes from a video that short features USGS Emeritus Research Ecologist, Cecil Schwalbe describing details of Gila monster biology and ecology and how he survived a very painful Gila monster bite.

Comparing genomes from 240 species to explore the evolution of placental mammals. The new phylogeny (black lines) has alternating gray and white shading, which distinguishes mammalian orders (labeled around the perimeter). Rings around the phylogeny annotate species phenotypes. Seven species with diverse traits are illustrated, with black lines marking their branch in the phylogeny. Sequence conservation across species is described at the top left. IMAGE CREDIT: K. MORRILL

Mario Apata and Anne Stone at the AABA meetings in Denver.

Infographic from WHO that says "Tuberculosis is the world's top infectious killer. TB caused 1.23 million deaths in 2024. Ending TB is possible. Fund it, research it, commit to it."

Anne at Winter Park

Mario giving his talk!

Picture of two researchers in the Huijben and Paaijmans labs who study resistance in mosquitos (that can spread diseases like malaria and West Nile virus). The caption says "I support ASU because the Center for Evolution and Medicine is bridging the gap between biology and medicine while empowering tomorrow's game changers by building a generation of future researchers and health professionals.

Anne Stone and Herman Pontzer at the AABA meetings in Denver just before Herman's plenary lecture.

Time-calibrated phylogenetic tree showing relationships between the extinct pampas wolf (Dusicyon avus) and the Falkland Islands Wolf (D. australis). Branches for D. avus are shown in orange and those for D. australis in red. Multiple ancient samples from each species cluster into two separate clades. The horizontal axis shows time in thousands of years before present (ka), from ~30 ka on the left to the present on the right. The two species are estimated to have diverged about 16,000 years ago. Additional gray bars show uncertainty in divergence times within each species. Source: Figure 3 of Austin et al. (2013) "The origins of the enigmatic Falkland Islands wolf" https://www.nature.com/articles/ncomms2570/figures/3

Phylogenetic tree of Mustelidae, most species in the genus Mustela groups on their own - but a few group outside closer to the American mink, these are the "American Weasels"

Time-calibrated phylogenetic tree of canids highlighting the position of the Falklands Wolf (Dusicyon australis). The tree shows that the Falkland Island Wolf clusters with the South American canids (including last 2025MMM combatant the maned wolf) rather than with Canis species or the red fox. Multiple Falklands Wolf samples form a tight clade. Branch lengths are scaled in millions of years before present, with divergence of major South American lineages occurring roughly 10-12 million years ago. A green shaded vertical band marks the formation of the Isthmus of Panama (~3 million years ago). Colored bars indicate phylogenetically informative polymorphisms shared by the Falklands Wolf, and a purple arrow marks the absence of a genetic insertion characteristic of South American foxes. Numbers at nodes indicate support values from the statistical analyses. Illustrations of representative canid species appear alongside the tree.

A DNA phylogeny of the extinct and living seals, including the extinct Caribbean monk seal which is grouped closest to the endangered Pacific monk seal, and then the critically endangered Mediterranian monk seal

Graph showing changes in effective population size (y-axis) through time (x-axis) for two Australian marsupials: the Ninu (pink lines) and the Yallara (beige lines). Both species maintain relatively large populations deep in the past, followed by declines beginning hundreds of thousands to millions of years ago. A shaded gray region marks the last glacial period, and vertical gray lines indicates the estimated divergence time between these species, around 3 million years ago. Source: Hogg et al. (2023) "Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial".

Map showing the habitats of the Mediterranian Monk seal, the Pacific Monk seal, and the extinct Caribbean Monk seal. None of their habitats overlap.

The maximum likelihood tree placing Mystacinidae in the same clade as Noctilionidae, a South American family of bats.

The support/conflict spectrum. The splits are numbered according number of data points supporting a specific split against those conflicting with it based on multiple trees. This can be misleading, however, as long terminal branches like Mystacina are conflicted because they are so unique and different relative to any other species.

Circular map of the mitochondrial genome of Camelus dromedarius. Colored segments around the circle mark different mitochondrial genes, including protein-coding genes (such as ATP6 and CYTB) thought to be involved in adaptation.

Phylogenetic relationships of West Indian oryzomyines. Consensus cladogram of four most-parsimonious trees (tree length, L = 1245; consistency index, CI = 0.37; retention index, RI = 0.64) of combined molecular (Irbp) and morphological characters. Jackknife (> 50%) and Bremer (> 1) nodal support indices are shown above and below branches, respectively. Clades A, B, C, and D are the same as those recovered by Weksler (2006). Out-groups include Peromyscus maniculatus (Neotominae), Nyctomys sumichrasti (Tylomyinae), and Delomys sublineatus, Thomasomys baeops, and Wiedomys pyrrhorhinos (Sigmodontinae). Oryzomyine generic taxonomy follows that of Weksler et al. (2006).

Map of the Windward and Leeward Islands of the Lesser Antilles, showing the distribution of extinct rice rats in Holocene archaeological sites (black stars) and Late Quaternary palaeontological sites (open circles), and islands from which rice rat species have been formally described. The modern-day sea level and 200 m isobath are both indicated, to show locations of shallow submarine banks that would have been exposed above water during Late Quaternary low sea-level stands, and which may have shared conspecific rice rat populations. Data from Pregill et al. (1994), Crock (2000), Newsom & Wing (2004), and LeFebvre (2007). -- and Martinique giant rice rat (‘Le rat pilori, Mus pilorides’), possibly drawn from life, from Gervais (1854: 411).

Sequence of the L. vexillifer alpha lactalbumin gene. The sequence is only about 3500 base pairs and the gene has four exons (shown in grey shading, with the amino acid sequence above).

A DNA phylogeny of the extinct and living hutias reveal they were all closely related. Today, there are 6 living and 5 extinct hutias, each used to live in their own Caribbean island.

Plotted radiocarbon dates (cal BP) for individual bones of hutia (Geocapromys ingrahami) from the Bahamian Archipelago. Samples on Eleuthera and New Providence in the Great Bahamas Bank all predate the black line at approximately 1,000 years BP, marks the time of colonization of the Bahamas Archipelago by the Lucayans. All other samples post-date 1000 years BP. Abaco is on the Little Bahamas Bank, Crooked Island is on the Crooked-Acklins Bank, Mayaguana was isolated through time, Providenciales is on the Caicos Bank .

Dorsal and ventral images of the skin of USNM 125345, a young thylacine adult male, which died in 1905 at the National Zoo; and was succesfully sequenced in our study as specimen 1

A DNA haplotype network that shows two Japanese otter individuals, one whic sits on its own lineage as if the Japanese otter is a separate species but one grouping with the other Eurasian otters as if they are not an isolated species

A DNA phylogeny of the extinct and living Eurasian otters where two individuals of the extinct Japanese otter form their own branch outside most other Eurasian otters except the Sumatran otter.

Time-calibrated phylogenetic tree showing evolutionary relationships among gazelles and related antelopes. The horizontal axis represents time from 17.5 million years ago to the present, spanning the Miocene, Pliocene, and Pleistocene. The genus Gazella forms a distinct clade that begins between 10 and 3 million years ago.

Scatter plot showing individual heterozygosity (a measure of genetic diversity) for multiple Australian rodent species. Each horizontal row represents a species. Points are colored by conservation status and population type: red for extinct species, yellow for extant species from small or geographically restricted populations, and gray for extant species from large or geographically connected populations. Extinct species appear near the higher end of the heterozygosity distribution rather than the lowest values, indicating that they did not show unusually low genetic diversity prior to extinction. Note that while Melomys rubicola was included in the study, it wasn't included in the analysis originating this specific image. Source: Roycroft et al. (2021) "Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement"

Time-calibrated molecular phylogenetic tree of Australian rodents based. Branches show evolutionary relationships among dozens of species across the Uromys, Conilurus, and Pseudomys divisions. Blue bars mark uncertainty in divergence times. Colored squares indicate conservation status (gray = least concern/near threatened, yellow = vulnerable/endangered/critically endangered, red = extinct --> this includes Melomys rubicola). A timeline at the bottom (x-axis) spans the Miocene to present. Illustrations of representative rodents appear along the right side.

Mitochondrial phylogenetic tree detailing the relationships among all available complete bovine haplogroup I, P, Q, R and T mtDNA genome sequences and five yak (B. grunniens) mtDNA genome sequences. The ancient auroch sequenced in this study is in haplogroup P, which sits outside the haplogroup for most domestics taurine cattle, haplogroup T.

European, North African and Near Eastern distributions of all the clades and subclades identified in Fig. 2. The circle area is in relation to the frequency of individuals belonging to a particular clade within a particular locality. Revealed (solid line) and inferred (dashed line) zone of contact between the western house mouse Mus musculus domesticus and the eastern house mouse Mus musculus musculus is shown.

Collection localities and mtDNA control region characteristics for all samples of house mouse Mus musculus domesticus from the British Isles and northern France (including published data). Colours indicate the proportion of individuals of each control region clade as defined in Fig. 2 (light green: clade C; red: subclade D1; pink: remainder of clade D; yellow: clade E; and blue: clade F). Squares show modern localities sampled in this study and stars show the locations for older museum material; the key to the numbering is in Table 1. Circles show previous published sequence data, including restriction fragment length polymorphism data for clade F.

Two-panel figure illustrating evolutionary traits and a genetic mutation in sea cows. Panel A shows a simplified phylogenetic tree of sirenians with three species illustrated at the top: the Florida manatee (Trichechus manatus), the dugong (Dugong dugon), and the extinct Steller’s Sea Cow (Hydrodamalis gigas). Along the branch leading to H. gigas, red markers indicate evolutionary traits including decreased blood-oxygen affinity and cold tolerance, among others. Panel B shows a DNA sequence alignment of the β/δ-globin gene region from sirenians, highlighting a nucleotide substitution that causes a Lysine-to-Asparagine change at position β/δ82 in Steller’s Sea Cow hemoglobin. Multiple H. gigas ancient specimens show the same mutation.

Bayesian consensus of Hyposmocoma showing 95% confidence intervals of posteriors . Numbers above branches
are Bayesian posterior probabilities (PP) and ML bootstrap values (BP), respectively. Coloured circles indicate microhabitat types and ancestral state probabilities.

Best Reduviinae tree based on RAxML analysis of 178 taxa using a partitioned molecular dataset of 5 gene regions (16S, 18S, 28S D2, 28S D3–D5, Wg). Bootstrap values are indicated on branches by colored triangles according to support strength. Reduviinae lineages are indicated as red branches and remaining reduviids as blue while outgroup taxa are black. The shaded red box highlights members of the hematophagous Triatominae, here shown as paraphyletic. Red arrowheads refer to the polyphyletic Cetherinae; the asterisk refers to Physoderinae nested within a reduviine clade.