Eduardo Amorim

@cegamorim.bsky.social

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Assistant Professor @ Arizona State University || School of Human Evolution and Social Change || Institute of Human Origins || Center for Evolution and Medicine|| March Mammal Madness @mmmletsgo.bsky.social || Amateur ceramist || #aDNA #PopGen

TOP: Fig. 1.Placement of study samples within the African crocodilian phylogenetic tree. Colours of the branches refer to the species found in Guinea-Bissau in this study, namely: the Nile crocodile (C. niloticus in green), the West African crocodile (C. suchus in yellow), and the West African dwarf crocodile (O. cf. tetraspisin purple). Red dots at the nodes represent highly supported nodes (>95% pp), coloured dots next to the branch description represent the samples collected for this study. The red rectangle in the inset map of Africa represents the geographic location of Guinea-Bissau. This figure and maps within it, were produced using QGIS version 3.36. BOTTOM: Fig. 2. Distribution of crocodile data collected in Guinea Bissau. Symbols with red strokes represent barcoded genetic samples.
A Representative ideograms of three main karyotypes (2n = 30/32/38) observed among the true crocodile species analyzed in the present study showing Zoo-FISH results after using CSI-1, OST-1, OST-4, and OST-19 probes, and the 18S rDNA distribution. Arrows indicate the 4 main chromosomal rearrangements involved in karyotype differentiation from a putative ancestral 2n = 32. B Ancestral state reconstruction of diploid chromosome number using maximum parsimony. The phylogenetic relationships were adapted from Oaks (2011) and Colston et al. (2020), C. halli was added manually, & its position requires confirmation. Karyological data were collected from Cohen & Gans (1970), Kawagoshi et al. (2008), Hekkala et al. (2011), Srikulnath et al. (2015), Oliveira et al. (2021), Olmo and Signorino (2022), and this study (in bold). The colored circles represent different 2n, while the black diamonds indicate the species with unknown 2n. Ambiguous data (marked with an asterisk) are addressed in the “Discussion” section of the paper.
(A) Geographic locations of non-invasive blow sampling (green dots) and invasive biopsy sampling for blow sampling validation (yellow dots) of humpback whales in Canada. (B) Image from a drone sent for blow sampling of a humpback whale. Scarring on the back of the whale was used for checking individual identification. (C) The drone used for blow sampling of humpback whales with custom attachments for holding a sterile petri dish for sampling. (D) An example of a blow sample from a humpback whale after collection by a drone but before processing by scientists.
Historic oil painting RCS 15 from the church with signs of biodeterioration on both sides. (A) Front side of the painting, (B–D) Back, (E–G) Stratigraphy of the painting under UV light. (E), the ground layer, the paint layer, and the surface of the varnish (F), and the ground layer and the paint layer (G), all with visible penetration of dark septate hyphae. Light and Scanning electron microscopy (SEM) (K–M) images show conidiogenous structures of Aspergillus on the back and massive growth on the front side of the painting.
a, Unrooted maximum likelihood phylogenetic tree showing the itraconazole MIC breakpoint and clinical or environmental source of isolation. b, Map showing the location of isolation for isolates included in this study, with the legend (bottom right) indicating the cyp51A polymorphisms present. c, Unrooted maximum likelihood phylogeny of all 218 isolates showing the genetic relationship between isolates. ‘Clade A’ and ‘clade B’ indicate the clustered nature of triazole resistance polymorphisms.
A) Frequency of species tree compared to alternative tree topologies, B) Divergence times of specific species tree topologies in windows, C) Possible signals of hybridization in the cats, and D) Relationship between recombination and phylogenetic discordance in windows across the genome.
Figure 1.(from Harvey 2014) —Chelifer cancroides (Linnaeus), living male from near Prebbleton, New Zealand (image courtesy of B. Donovan).
Fig. 3. Documentation of venom release in C. cancroides after electrical stimulation of the chelal hand. The flow of current was facilitated by a conductive fluid (CF). A liquid indicator (LI) was used for the experiments to visualize venom release. A, B) Venom extraction using Type 1 capillaries with larger inner diameter. These capillaries partially cover the movable finger (MF) while the venom (V) is being collected. Before electrical stimulation, the movable finger is in a relaxed state (A). When electrical power is applied, the venom tooth pinches the glass wall of the capillary, causing the release of venom (B). C, D) Venom extraction from the fixed finger using Type 2 capillaries with an inner diameter of about 10 μm. These capillaries covered only the venom tooth and lamina defensor. The application of electricity caused the immediate release of venom, which replaced the brownish liquid indicator at the tip of the capillary.
Fig. 1. from Armstrong et al. 2024; Left: Map showing the location of gray fox samples used in some genetic studies and the location of our new reference genome from Vermont, overlaid on the current gray fox range (IUCN). Map sources: Esri, USGS, and NOAA. Right: A gray fox explores a commonly used hiking trail on the Middlebury College campus (photo by Andrew Ng, Middlebury College).
The mitochondrial genome of Liposcelis bostrychophila. The directional transcription is indicated with arrows. Protein-coding and ribosomal genes are shown in white with standard abbreviations. tRNA genes are abbreviated by a single letter with dark gray except the 2 serine and 2 leucine tRNAs: S1 = AGN, S2 = UCN, L1 = CUN, and L2 = UUR. The non-coding regions >50 bp are indicated in black. IR, an identical region in mt chromosome I and mt chromosome II. The four pseudogenes and their corresponding position in the putatively functional genes are indicated by the number I, II, III, and IV.
Figure 3. (from Borkenhagen & Krupp, 2013) Ventral view of the head and chest. A Carasobarbus apoensis (SMF 30167, 108.6 mm SL) B Carasobarbus canis (SMF 33135, 108.3 mm SL) C Carasobarbus chantrei (SMF 33133, 122.9 mm SL) D Carasobarbus exulatus (SMF 33109, 103.7 mm SL) E Carasobarbus fritschii (SMF 33446, 89.6 mm SL) F Carasobarbus harterti (SMF 33368, 93.6 mm SL) G Carasobarbus kosswigi (SMF 30173, 107.1 mm SL) H Carasobarbus luteus (SMF 30176, 120.7 mm SL) I Carasobarbus sublimus (SMF 33118, 80.2 mm SL), pictures resized to facilitate comparison.
Dated phylogeny of hemipteroid insects (Hemiptera, Thysanoptera, and Psocodea) based on maximum likelihood analysis of a supermatrix of first and second codon position nucleotides corresponding to 859,518 aligned amino acid positions from transcriptome or genome sequences of 193 samples. Colored circles indicate bootstrap support.
Adapted from Axelsson et al. 2013 Fig 2c: Histogram showing the distribution of diploid amylase copy number in wolf (n=35, blue) and dog (n=136, red). Dogs carry more copies of the starch-digesting gene AMY2B than wolves. Additional copies make dogs better than wolves at digesting starchy foods like grains & vegetables.
Fig 1 (from Arash Jouladeh-Roudbar et al. 2024): Distribution map of Carasobarbus species in Persian Gulf basin.
Loss of migratory behaviour in the white stork Ciconia ciconia. (a) Increased food availability, particularly at landfills, is one of the major factors promoting an increase in the wintering population of white storks in Europe . (b) Population trends of wintering white storks from the Portuguese population between 1995 and 2020. (c) Changes in the percentage of resident white storks in Portugal in the last 25 years.
Fig. 1. (From Alves et al. 2019) Rabbit origins and sampling locations. Historical (circles) and modern (triangles) sampling locations. Dates in red inside the maps show the date of the first myxomatosis outbreak in the respective countries. Orange dashed arrows and dates reflect historical and archaeological records of the colonization of European rabbits from France to the United Kingdom and Australia.
Recent progression of house mice from Western Europe to Eastern North America. Hypothesized colonization history of house mice in Eastern North America showing divergence times as inferred from demographic modeling. Black dashed arrow illustrates migration of house mice from Western Europe to eastern North America.
Fig 2 (from Alves et al 2015): Reduction of genetic diversity along the rabbit domestication route. Each of the 45 circles represents a single microsatellite coloured according to the proportion of the expected heterozygosity per microsatellite present on its respective population. Note that the two wild samples (Iberian Peninsula and France) are proxies for the ancient wild samples that were involved in colonization of France and domestication. Shaded areas indicate the different bottleneck events that occurred at the colonization of France, initial domestication event, and breed formation. Values aside arrows show the amount of genetic diversity lost in each event estimated using a resampling methodology (See Methods).
A) Ventral thorax of Lepisma saccharinum (Spain): coxae (1) with rounded scales; femora (2) and tibiae (3) of the first and second legs lack scales and bear only setae. Scale: 0.25 mm. B) Ventral view of the second leg of Ctenolepisma villosum (Spain): coxa and femur with rounded scales; tibia without scales, bearing only setae. Scale: 0.1 mm. C) Ventral femur of Ctenolepisma rothschildi (Cape Verde) with modified scales (subtriangular, distally truncated, variable). Scale: 0.2 mm. D) Lanceolate scales on the ventral femur of Ctenolepisma lineatum (Spain). Scale: 50 μm.
Detection of cellulase activity in digestive fluids of Thermobia domestica and Ctenolepisma longicaudata. Zymograms with 0.2% carboxymethyl cellulose were used to detect the cellulase (CMCase) activity in head, foregut, midgut and hindgut tissues of T. domestica (left) and C. longicaudata (right). MM, pre-stained protein molecular marker; +ve, commercial cellulase used as positive control; H, head; FG, foregut; MG, midgut; HG, hindgut.
Fig 1. from Graciá et al 2013. Distribution of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsula. This species can be considered continuous across the Iberian Peninsula, with the exception of the coastal region in the center and north of Portugal, and Galicia and the Cantabrian coasts in Spain. The number of analysed chicks (N) in each subpopulation is indicated.
Genome-wide screens highlight changes in genes that are potentially involved in exceptional immunity in bats. a, Inactivation of the immune-stimulating genes LRRC70 and IL36G. Boxes represent coding exons proportional to their size, overlaid with gene-inactivating mutations present in six bat species. Scale bar, 100 bp. b, Diagram showing the canonical NF-κB signalling pathway (purple) and interacting proteins that have experienced positive selection or have been lost in bats.
Graphical abstract with map showing arrival in China no earlier than 600CE
Parallel evolution of prestins of echolocating bats and bottlenose dolphin. The species tree of 18 mammals. Tree branches are not drawn to scale. Parallel substitutions were examined between the red branch and the branches labeled 1, 2 and 3. The amino acid (N: Asn; T: Thr) at position 7 of prestin is shown for each interior and exterior node.
Survival limit of DNA, as inferred from studies described in present paper, compared to chronology (El Mahdy, 1989) of Pharaonic Egypt.
Fig. 1. Maximum likelihood (ML) phylogram for Crocodylus based on mtDNA sequences (complete matrix). The topology is identical to that supported by Bayesian analysis; white circles at nodes mark clades with 100% ML bootstrap support & posterior probabilities of 1.0. The scale bar is proportional to 0.01 substitutions/site. New World Crocodylus species form a monophyletic group, as do Asian + Australian Crocodylus species, but C. niloticus is paraphyletic. According to mtDNA results, “eastern” Nile crocodiles are more closely related to the 4 New World species than to “western” Nile crocodiles. The 8 new mtDNA sequences generated for this study are indicated by gray rectangles overlaying terminal taxon names. The 3 background colors separate New World species of Crocodylus (represented by the painting of C. rhombifer – top), African lineages (C. niloticus – middle), & Asian–Australian species (represented by C. johnstoni – bottom). The tree includes multiple representatives for some species, & these are numbered. The tree is rooted with mt sequences from Mecistops and Osteolaemus (not shown).
Geographical distribution of the 22 sampling sites of Cyperus papyrus in Southeast Africa and the Bayesian genetic clustering of individuals based on 19 microsatellite loci (B). A The geographical distribution of sampling sites onto the river basin shape file obtained from the Hydrologic Derivatives for Modelling and Analysis (HDMA, https://hidrosheds.cc.usgs.gov/hydro.php). Different river basins are highlighted by different colours following the legends. B Geographical distribution of the genetic clusters (K = 4). Each colour represents an inferred genetic cluster. The size of cluster chart section represents population co-ancestry for each cluster. The plot shows the individual ancestry for the most likely K = 4. Details of the populations are provided in Supplementary Table S1.
Figure 2 in Louis et al. (2020). Mean nucleotide diversity (π) from published, population-level cetacean mitogenome studies from the Arctic and elsewhere. Dark dots indicate range-wide data and grey dots local data. The number of samples comprising each dataset is shown. Cetacean illustrations by Uko Gorter.
Figure 1 from Louis et al. (2020). (a) Map of sampled narwhal stocks. Three stocks comprise several sample localities: Eastern Baffin Island, Eclipse Sound and Somerset Island. The summer and winter distributions have been re-drawn from the latest NAMMCO report. Note that a recent study indicated that narwhals between North-East Greenland and Svalbard are present year-round(b) Median-joining haplotype network of the 64 haplotypes found within the 121 narwhal mitogenome sequences. Each circle represents a haplotype and is coloured in proportion of individuals from each stock, where the haplotype is found. Circle size is proportional to haplotype frequency. Black circles indicate intermediate haplotypes not found in our samples. Black dashes indicate mutation steps between haplotypes; of note, distances between haplotypes are not to scale. Narwhal illustration by Uko Gorter.
Population structure among polar bears. Principal components analysis using (A) 20 microsatellite loci from 372 Greenland polar bears versus latitude, (B) whole genome sequences from 40 polar bears, and (C) whole-blood transcriptomic data from 16 polar bears. (D) Clustering analysis of 3,064 polar bears assuming 4 clusters where each vertical bar corresponds to an individual. (E) Summary of the clustering results in (D) by subpopulation. SEGz, Southeast Greenland; NEG, Northeast Greenland; BS, Barents Sea; KS, Kara Sea; CS, Chukchi Sea; SB, Southern Beaufort; LP, Laptev Sea; NB, Northern Beaufort Sea; VM, Viscount Melville Sound; MC, M’Clintock Channel; GB, Gulf of Boothia; LS, Lancaster Sound; NW, Norwegian Bay; KB, Kane Basin; BB, Baffin Bay; DS, Davis Strait; FB, Foxe Basin; SH, Southern Hudson Bay; WH, Western Hudson Bay.
Admixture between polar and brown bears estimated using Dfoil. a Schematic of the tested topology, assuming brown bear MRCA is more recent than polar bear MRCA. Analyses used three females per P1, P2, and P3, with transversions in 200-kb autosomal windows. b Dfoil results from independent runs (n = 3×3×3 for polar P3; n = 3×3×1 for LCA as P3). Each run included 11,575 autosomal windows. Arrows on the x-axis show inferred gene flow direction; bidirectional arrows indicate undetermined direction.
Annual physiological cycles in grizzly bears. a Metabolic stages—hibernation, active, and hyperphagia—mapped across months; blue line marks insulin resistance period. Arrows indicate sampling points from adipose, liver, and muscle of six captive bears at WSU Bear Center. Photo: Donald Montemorra. b Body weight across sampling points (*p < 0.05; Supplementary Table 5). c Body temperature across sampling points (**p < 0.01; N = 6; Supplementary Table 6). Mean, SD, and individual values shown. d Same bear photographed post-hibernation (April) and pre-hibernation (October) at WSU Bear Center
Part of Figure 1 from Baniel et al. (2022). Gut microbiome taxonomic assembly in the first 3 years of life in immature geladas (A) Relative abundance of the 15 and 19 most abundant phyla and families per age category. (B) Age-associated pattern of alpha diversity (Shannon index of ASVs) within samples. The dotted vertical line represents the critical point of inflexion (7.3 months, 95% CI = [6.4–8.2] in shaded gray, nonlinear quadratic plateau model [QPM]: R2 = 0.62) representing the age at which alpha diversity converges to adult-like patterns. Immatures are considered ‘‘weaned’’ when their mother has resumed reproductive cycles. The dataset was rarefied at 20,000 reads for the figure. (C) Age-associated pattern of beta diversity. A principal component analysis (PCA) was used to ordinate samples based on the Aitchison dissimilarity index. (C) represents the projection of the first principal component (PC1) that is best explained by the age of immatures. The dotted vertical line represents the critical point of inflexion (17.2 months, 95% CI = [15.5–19.4] in shaded gray, nonlinear QPM between PC1 and age: R2 = 0.55) representing the age at which immatures beta diversity (i.e., overall composition) converges to adult-like patterns.
Distribution of mtDNA haplotypes across the majority of the pumas range. Pie charts refer to mtDNA haplotypes specific by 16 single nucleotide polymorphisms defined in pumas
Network of Addax mtDNA haplotypes. Circles represent haplotypes, with most likely evolutionary relationships indicated by solid black lines and alternative likely relationships shown by dashed grey lines. Mutational steps are shown by hashes. Results indicate that the haplotypes from wild populations are more diverse than those of ex-situ groups.
The spotted gar (Lepisosteus oculatus), which diverged from teleosts before the teleost genome duplication and retains a genome more similar to tetrapods, provides a valuable comparative model for studying vertebrate retina evolution. Histological comparisons using H&E staining show that the overall retinal structure of gar resembles that of both zebrafish and mouse.
Simplified phylogeny of gnathostomes (topology from refs 27, 28) showing published data on the distribution of surface tissues on the odontode skeleton. Black branches, names and text indicate extant taxa; grey branches, names and text indicate fossil taxa. The surface tissues of Psarolepis and Andreolepis are discussed in the text.
Representation of 12 pseudochromosmes of Ginkgo biloba. The tracks from outer to inner circles represent the pseudochromosomes (Mb), syntenic relationship between the genetic map and genome assembly, heterozygosity (blue, 0–0.77%), percentage of fragmented LTR sequences (red, 0–63%), percentage of intact LTR sequences (green, 0–11%), gene density (purple, 0–28%) and syntenic block.
Phylogenetic tree showing approximate divergence times across different mustelids in the subfamily Guloninae and other carnivores.
Timescale of carnivoran diversification, based on the Thorne/Kishino relaxed molecular clock method, incorporating 21 fossil calibrations (similar results were obtained with BEAST – see Fig. 3, Table 6 and Supplementary Information). The tree is a cladogram with node depths (branch lengths) drawn proportional to time, with a timescale shown at the bottom, including the paleontological epochs of the Cenozoic Era (Paleoc. = Paleocene; Pi = Pliocene; Pe = Pleistocene). Family names are indicated on the right, as are the major suborders Feliformia and Caniformia. Numbers above nodes are divergence ages in MYA (millions of years ago); only nodes defining families or higher clades are labeled (the only exception is the New World sub-clade of the Mephitidae, mentioned in the main text); see Table 6 for point estimates and credibility intervals for node ages estimated with Divtime and BEAST.
Phylogeny of the world’s otters -- For the 11 species represented by modern samples (solid terminal branches), a genome-wide species tree was inferred with ASTRAL-III from maximum likelihood (ML) phylogenies of non-overlapping genomic fragments (GFs). All four combinations of GF size and spacing (see text and Table S2 for details) yielded the same most common tree. In the four ASTRAL-III trees, all nodes were supported by 100% bootstrap values. Numbers above branches are estimated divergence times for the adjacent nodes, calculated as the mean value across all GFs. Species with dashed terminal branches were represented by museum specimens and had lower depth of coverage.
In primitive forms, the superficial masseter arose near the anterior end of the toothrow (a bump that serves as the point of origin in many rodents is termed the masseteric tubercle) and inserted along the lower part of the mandible at the rear. The lateral masseter arose from the midportion of the zygomatic arch and also inserted along the bottom of the lower jaw towards its rear. The medial masseter was small, originating along the inside of the middle of the zygomatic arch and inserting on the mandible near the end of the molar toothrow. This condition is called protrogomorphous and in living rodents, is seen only in aplodontias.
Maximum-likelihood phylogram inferred from nonredundant haplotypes from 380 samples sequenced for the first 450 bp of cytochrome b (Cytb). This tree is the same topology as a tree inferred from nonredundant haplotypes from 112 samples sequenced for 1,050 bp of Cytb with the exception of phylogeographic resolution within Aplodontia rufa rufa (see inset with bootstrap support). These 2 data sets have different samples representing the tips of the trees but infer the same clades and overall topology. Bootstrap support ≥ 70 is indicated with ○, whereas support ≥ 90 is indicated with •. The 1st symbol represents bootstrap support estimated from the first 450 bp of Cytb and the 2nd symbol is the bootstrap from the 1,050 bp of Cytb. The 3rd symbol represents the posterior probability from the Bayesian analysis ≥ 0.95. Outgroup taxa relationships are collapsed in this figure for ease of presentation. State(s) where samples were collected are designated in parentheses.
Chromosome painting analysis of the Chacoan peccary showing the autosomes (1-9) and the two sex chromosomes.
Structure plot showing how genetic data for muskrats in maine (ME), new hampshire (NH), and Appledore Island (Shoals) groups into two (top) and three (bottom) clusters. Results show that the mainland populations (ME and NH) are distinct from Appledore Island.
Principal component analyses (PCA) of microsatellite data for muskrats across their North American range. Three clusters are shown, representing an Eastern cluster, a Western cluster, and a cluster from Newfoundland, respectively.
Population structure in Maned Wolves based on mitochondrial DNA (mtDNA) sequences. The figure has three panels. [top-left] Minimum-spanning network of mtDNA genes. Circles represent the different haplotypes and circle sizes are proportional to the haplotype’s frequency in the population. [right-hand side] Map of South America highlighting the sampling localities. Argentina (Blue), Bolivia (Red), Brazil (Yellow), and Uruguay (Purple). [bottom-left] Table showing numbers and distribution of mtDNA haplotypes within each of the four geographic groups/countries.
A phylogenetic tree of different strains of rabies. Unless labeled with a species (e.g. raccoon, bat), the tree is showing that most rabies virus cluster according to region, regardless of whether they are within canids or mongoose. However, the African mongoose strain forms a monophyletic cluster, shown in purple.
Location map and sample sites used in this study of the quokka, Setonix brachyurus. Sites underlined were trapped but contained no quokkas. Towns are shown in bold and are depicted by filled circles. The northern jarrah forest is shaded grey and the Darling Range generally runs along its western boundary. The 1,000 mm (dashed) and 700 mm (dotted line) annual rainfall isohyets are also shown.
Phylogenetic tree showing relationships between mongoose using nuclear and mitochondrial markers. Different colors represent different clades and the marsh mongoose clade is highlighted in green.
Alignment depicting part of exon 2 of LWS in afrotherian taxa. Deleterious mutations are highlighted with rectangular boxes. WGS = whole genome sequence; PCR = PCR sequence
Retinal protein networks in Chrysochloris asiatica (golden mole), Heterocephalus glaber (naked mole-rat) and Condylura cristata (star-nosed mole). A. Phototransduction; B. Visual cycle
Phylogenies of the mitochondrial genome, the X chromosome, the autosomes (chromosomes which are not X or Y) and the Y chromosome of different Felid groups. The trees show different arrangements, indicating complex evolutionary histories that include hybridization and rapid speciation.
Autosomal karyotypes for six genera of hares and rabbits. Darker regions are indicative of AT-rich regions and generally tend to be more gene poor.
Phylogenetic tree of lagomorphs including the Hispid hare. Supermatrix ML phylogeny derived from all seven gene fragments used in the present study. Arrows indicate unique insertions/deletion supporting associations. Nodes are labeled A to G and correspond to those in Table 5. Values above and below nodes represent the nodal support (MP = maximum parsimony bootstrap; ML = maximum likelihood bootstrap; and BI = bayesian inference posterior probability) for associations among the 25 ingroup taxa. An asterisk indicates that the node was not supported by > 50% bootstrap support.