Lucas R Moreira

@lucasrocm.bsky.social

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Evolutionary biologist interested in how the genome works and which changes lead to phenotypes. Computational Scientist at Colossal Biosciences 🦤

Graphical abstract showing effect of deletion compared to wild-type coloring
Images of non-charcoal (left) and charcoal (center and right) Bengal cats, with corresponding genotypes at Asip and Mc1r. lc and dom superscripts, refer to the normal leopard cat and normal domestic cat alleles, respectively, and a refers to the Asip nonagouti allele.
Principal component analysis of modern lions (blue square), modern tigers (green diamonds), and cave lions (red circles) showing the position of the japanese tigers (yellow stars). Cluster positions indicate that japanese "tiger"s are actually cave lions.
Admixture bar plot showing genetic structure across 27 named dromedary camel-types from Asia and Africa at multiple clustering levels (K = 2, 3, 5, 10, 16). Each vertical bar represents one individual, colored by proportional membership in genetic clusters. Vertical white lines separate camel-types labeled above, with country abbreviations below (on x-axis). At K = 2, individuals broadly separate into two main groups corresponding to African camel-types (e.g., Borena, Rendille, Turkana, Gabbra) versus most others, with Omani camels already distinct. At K = 3, three main clusters emerge: a unique Omani group, a distinct African group, and a third group containing remaining camel-types. At higher K values, additional substructure appears within some camel-types (e.g., Hadana, Awarik, Awadi, Pakistani Kohi and Raidi, and Majaheem), but many individuals show mixed ancestry, with colors spread across camel-types. Overall, the plot illustrates that genetic clustering aligns more strongly with geographic origin than with named camel-types, which often do not form clearly distinct genetic groups.
Map of Europe showing the complete mtDNA genomes in modern cattle breeds reported as blue branches (lineages T, Q and R) and ancient auroch mtDNA genomes reported as green branches (lineages T, P and E). The Northern European Aurochs have lineages P and E but the Southern European aurochs also have liineage T, which is the most common lineage in modern cattle.
Schematic diagram of a camel kidney medullary collecting duct cell showing molecular responses to dehydration. The cell is bordered by tight junctions, with the urinary lumen on the left and renal interstitial fluid on the right, where osmotic stress occurs. Red labels indicate upregulated genes (relative to the mammal standard), green indicate downregulated, and white indicate unchanged expression. Water reabsorption occurs through aquaporins (AQP2 on the lumen side and AQP3 on the interstitial side). Sodium is reabsorbed via ENaC and potassium is secreted via ROMK, while Na⁺/K⁺ ATPase maintains electrolyte balance. Inside the cell, increased glucose uptake through GLUT1 fuels glycolysis and ATP production, supporting ion transport. Glucose is also converted into sorbitol via aldose reductase (AR), contributing to osmotic balance. NFAT5 regulates osmotic stress responses, but transporters for taurine, betaine, and myo-inositol (TauT, BGT1, SMIT) are downregulated, indicating reduced osmolyte import. Instead, organic osmolytes such as sorbitol and glycerophosphocholine (GPC) accumulate through metabolic pathways. Additional components include antioxidant responses (Nrf2), reactive oxygen species (ROS), and metabolic enzymes (SDH), all contributing to maintaining water and osmotic homeostasis under dehydration. Source: Wu et al. (2014) DOI: 10.1038/ncomms6188
Genetic diversity and demographic history of vultures. (A) Comparison of genome-wide heterozygosity in birds. (B) Demographic history of the two vultures (G. himalayensis and G. barbatus). Genomes of three individuals of G. himalayensis and one individual of G. barbatus were analyzed. Tsuf, atmospheric surface air temperature.
Summary of the 33 microvirus genomes identified in this study and their distribution across 14 Gila monster fecal samples. The solid dark-gray and black circles indicate 95% to 99% and 100% raw read genome coverage, respectively, per Gila monster fecal sample. The number of reads that mapped to the microvirus genome sequence and the depth of the read coverage are summarized, and the sample containing the highest number of reads for each microvirus is denoted by a black circle with a yellow outline. The genome organization is provided on the right with color-coded, open reading frames with details of putative protein families.
Map showing the past (grey) and current (black) distribution of the species, based on Mundy et al. (1992) and Heredia & Heredia (1991). Pie diagrams depict the proportions of clade A (black) and clade B (white) haplotypes in different bearded vulture populations. Numbers in parenthesis refer to sample size.
(A) Phylogenetic tree of 12 mammals used in this comparative analysis with red lines corresponding to the branches of long-lived mammals that are less prone to cancer (Asian elephant, African bush elephant, greater horseshoe bat, and naked mole rat). (B) Alignment of the ALDH6A1 protein sequence across species, where Asian elephant, African bush elephant, greater horseshoe bat, and naked mole rat have one mutation (asterisk) in the Aldehyde dehydrogenase domain (in red) that differs from other mammals that all the T (Threonine) residue (in black). (C) 3D structure of ALDH6A1 protein in long-lived mammals vs. short-lived mammals.
A graph showing probability distribution curves for fossil remains from different species: hippos in red and yellow, mammoths in grey, woolly rhinos in blue. Time since the present is on the x-axis. Hippo fossils cluster between 47k and 31k years ago.
Sampling locations of Asian elephants included in the study (colored dots) as well as the geographic distributions of elephants in India (grey shading) and potential geographic barriers to elephant dispersal in India (blue and black lines). Sampling locations include northern populations in Northwestern India (NW; pink) and Northeastern India (NE; red); a central population in the Central Indian landscape (CI; blue); and southern populations in the north of Palghat Gap (NPG; orange), south of Palghat Gap but north of Shencottah Gap (SPG; green), and south of Shencottah Gap (SSG; yellow).
Photos by Rebecca Raymond/National Park Service and Dan Stahler/National Park Service: Both of these Yellowstone wolves display the hair loss and skin lesions associated with mange. By analyzing 25 years of wolf observations and genetic samples from 408 Yellowstone wolves, a Princeton-led research team found that genetics play a role in the severity of the mite-borne disease. They found support for the “monoculture theory”: wolves with severe mange, like the one on the left, tend to have less genetic variation than wolves with mild symptoms, as seen on the right.
Figure 6. (Sacks et. al 2022) Schematic representation of a hypothesis explaining the origins of island foxes (Urocyon littoralis) from a mainland ancestor replaced by expanding populations of gray foxes (U. cinereoargenteus). Island foxes and their immediate mainland ancestors (green) are distinguished from gray foxes (blue) 15,000 years ago (YA), prior to their introduction to the northern super-island, Santarosae 13,000–9500 YA, followed by their independent introductions to each of the southern islands 6000–200 YA, and finally their extirpation and replacement by expanding gray foxes on the mainland during the late Holocene. Overlapping time intervals reflect uncertainty in timing of extirpation and replacement. Putative introductions of foxes to the Channel Islands are indicated by green arrows and putative expansion routes of gray foxes are indicated by black arrows. Dashed lines indicate boundary to the California Floristic Province and dotted line bounds the Central Valley.
Table 3. Population Aggregation Analysis (PAA) Assigning Archival Specimens to Western or Eastern Clade. Diagnostic nucleotide positions within the short 12s (11 sites) and d-loop (14 sites) sequences. Specimens in bold represent archival material. Eight mummy specimens are highlighted in grey, all correspond to the western lineage. Sequences with question marks across one marker represent failed amplification success for that specimen. D-loop site 206 is an indel event in the eastern clade. The miscoding error observed at d-loop site 226 due to DNA degradation
Venn diagram of candidate loci identified by multiple outlier detection techniques. Shown are the number of candidate loci identified by each software. LFMM approach is colored in yellow for the abiotic variables and in green for the biotic variables.
(A) FACS analysis of blood leukocytes before and after antigen/mitogen cocktail immunostimulation. (B) Immunostimulated leukocytes. Scale bar, 10 µm. (C) VLR Virtual northern blot. Amplified cDNA from larval tissues, or sorted cells from unstimulated and immunostimulated blood and haematopoietic organs. Molecular size is indicated in kilobases. (D) VLR stick model. Sections from left to right are: signal peptide, N-terminal LRR, nine LRRs, connecting peptide, C-terminal LRR, threonine/proline-rich stalk, GPI anchor and hydrophobic tail (E) Epitope-tagged VLR and FcγRIIb (control) expressed in mouse thymoma cells, treated with (+ PLC) or without (- PLC) GPI-phospholipase C. (F) Three-dimensional model of VLR diversity region (two rotations).
Figure 3. Phylogenetic analysis of RABVs analyzed in this investigation. A 592-nucleotide region encompassing the cytoplasmic domain of the glycoprotein and the G-L intergenic regions of the RABVs included in this study together with other previously characterized viruses was used in the analysis. A neighbor-joining tree of the G-L intergenic region sequences illustrating the genetic relationships of canid rabies viruses from the Kromdraai region of Gauteng. The virus sequences were compared with those from jackals from the 2016 rabies outbreak [14]. The virus sequence of the honey badger RABV is highlighted in red. The horizontal lines are proportional to the evolutionary distances between sequences and the scale bar represents nucleotide substitutions per site.
Demographic reconstruction of Baiji populations over time show that their populations had declined up to 10,000 years ago, at the beginning of the Holocene, and then had began to recover until human activity drove them extinct.
Phylogeny of the river dolphins, where the East Asian Baiji was more closely related to the genus Inia, the South American river dolphins, including the La Plata river dolphin in the genus Pontoporia than to any of the Eurasian dolphins.
Figure showing 2 phylogenetic trees of Tethytheria (Steller's Sea Cows and relatives) based on complete mitochondrial genomes: (A) top plot shows a Neighbor-Joining tree and (B) the bottom plot a Maximum Likelihood tree. In both trees, the extinct Steller’s Sea Cow (Hydrodamalis gigas) clusters most closely with the dugong (Dugong dugon), forming a sister group within Sirenia, while manatees (Trichechus manatus) branch off earlier. More distantly related species (Asian and African elephants, as well as woolly mammoth), form separate lineages. Branch lengths represent genetic divergence, and nodes on the Neighbor-Joining tree are supported by high bootstrap values. Procavia capensis is used as an outgroup in both cases. Source: Sharko et al. (2019) Genomics.
This bar graph displays the variety of different repeat lengths found within the pSS(R)2 sequence. It shows that the fragment is composed of short sequences of DNA ranging from 2 to 17 nucleotides long
A map of sites where samples of greater one-horned rhinoceros (Rhinoceros unicornis) dung were collected in Gorumara National Park, West Bengal.
A diagram showing for six species of whale (humpback whale colored in light orange) the enrichment of mammalian phenotype categories for positively selected genes in each species.
Heterozygosity of the various mink and weasels painted as a heat map. More genetic diversity is painted yellow, less is painted blue. The American mink, the closest relative to the Sea Mink, has internediate to low levels of heterozygosity.
Current distributions for all weasels in the western hemisphere : (A) M. erminea, (B) M. frenata, M. africana , M. felipei , (C) M. vison, (D) M. nigripes , M. nivalis
Line graph showing historical effective population size (y-axis) over time in years before present (x-axis) for 3 camel species: Camelus bactrianus (black), C. dromedarius (blue), and C. ferus (red). All three species show a similar pattern: population sizes increase in the distant past, then decline sharply by up to ~70% during the last glacial period (LGP, shaded), with a minimum around the last glacial maximum (LGM). Afterward, populations partially recover, with C. bactrianus reaching the highest recent values, C. ferus intermediate, and C. dromedarius remaining lowest. Small camel illustrations appear next to each trajectory.
Relative proportions of crown divisions in extant genera of tribes of Neotominae following the interpretation of Koenigswald (2020). Relative lengths of differentiated roots of some taxa not available due to breakage or buried in alveolus. Numbers correspond to the following genera: 1, Neotoma; 2, Ochrotomys; 3, Scotinomys; 4, Baiomys; 5, Isthmomys; 6, Reithrodontomys; 7, Onychomys; 8, Acrolophomys; 9, Habromys; 10, Megadontomys; 11, Neotomodon; 12, Osgoodomys; 13, Peromyscus; 14, Podomys.
Divergence times tree for Neotominae subfamily based on a concatenated analysis of the mitochondrial protein-coding gene cytochrome-b, and intron 2 and parts of exons 2 and 3 of acid phosphatase type V, intron 2 of the alcohol dehydrogenase gene, exon 6 of the protein-coding dentin matrix protein 1 gene, intron 7 of the beta-fibrinogen gene, exon 10 of the growth hormone receptor, single exon of the recombination activation 1 gene, and the first exon of the nuclear gene interphotoreceptor retinoid-binding protein. Divergence date estimates are indicated in millions of years. Bars indicate the minimum and maximum date at the 95% highest posterior density for node height (95% HPD). -- Photo: https://www.mammaldiversity.org/taxon/1002266/
Fig. 6. A, Northern blot analysis of 20 μg of total cellular lizard RNA from intestine (I), liver (L), pancreas (P), and salivary gland (S) hybridized with the lizard exendin cDNA probe. The ethidium bromide-stained gel and the positions of 18 and 28 S ribosomal RNA are shown. B and C, Southern blot analysis of H. suspectum genomic DNA hybridized with a lizard exendin cDNA probe (B) or a lizard proglucagon cDNA probe common to both lizard I and lizard II cDNAs (C). H. suspectum genomic DNA (20 μg) was digested with BamHI (B), EcoRI (E), or HindIII (H). The relative sizes of the DNA fragments were determined from a coelectrophoresed DNA ladder shown at the left in kilobases.
Phylogenetic tree showing relationships among gazelle species based on a mitochondrial DNA gene (cytochrome b). Multiple samples labeled as “putative G. saudiya” (captive individuals) cluster with other species such as G. subgutturosa, G. bennettii, and G. dorcas, rather than with confirmed G. saudiya specimens. True G. saudiya samples (including museum specimens labeled “G. saudiya A” and “B”) form a separate branch. This demonstrates that many captive gazelles previously identified as Saudi gazelles are genetically different species and are thus irrelevant to the conservation of G. saudiya.
Phylogenetic tree of gazelles showing their evolutionary relationships alongside inferred geographic origins. Each species is labeled on the right. Colored squares along the branches indicate the most likely ancestral geographic range: Africa (red), Middle East (yellow), Central Asia (blue), and India (green). An inset map at the bottom illustrates the four regions, highlighting how gazelles originated in the Middle East and dispersed into Africa, Central Asia, and India over time.
Two-panel figure linking gene mutations to skin traits in Steller’s Sea Cow (Hydrodamalis gigas). Left: diagrams of the lipoxygenase genes ALOXE3 and ALOX12B, showing protein domains (PLAT and lipoxygenase) and multiple premature stop mutations; those specific to Steller’s Sea Cow are highlighted in red, indicating gene loss-of-function. Additional truncating mutations known from humans are shown in black. Right: illustration of Steller’s sea cow with thick, rough, bark-like skin.
Demographic trajectory over time for thylacines and Tasmanian devils show their populations had been declining slowly since before human arrival to Australia and the isolation od Tasmania from the mainland
Phylogenetic relationships amongst immunoglobulin (Ig) domains thylacine, Tasmanian devil, koala, opossum, human, and mouse. Ig domains have expanded in the thylacine similar to other marsupials and show little to no orthology with eutherian Ig domain sequences.
Frequency and distribution of the haplotype R. It is found only in Italy where is represents up to 3% of cattle haplotypes in the central and South of Italy
Haplotype diversities of 4 focal species compared to more abundant lizard species from Mojave National Preserve. Error bars represent ± 1 standard error. Abbreviations: cytb, cytochrome b; CARD4, caspase recruitment domain gene 4; MC1R, melanocortin 1 receptor gene; RAG1, recombination activating gene 1.
Germline nuclei contain more DNA than somatic nuclei. Flow-cytometric analyses of nuclear DNA content reveal major differences in nuclear DNA content between germline (spermatids) and somatic tissues. This figure shows sperm and blood traces from two different animals. Blue and red arrows mark the relative sizes of 1C sperm (2.31 pg) and 2C blood (1C = 1.82 pg) genomes, relative to arbitrary fluorescence units.
Haplotype diversities (h) for the cytb, MC1R and RAG1 genes for four species of lizards from the Mojave National Preserve. Error bars represent 95% confidence intervals around the point estimates of h. *Indicates statistically significantly higher diversities for comparisons between high- and low-density species based on confidence interval overlap (Cumming and Finch, 2005). An additional asterisk indicates statistically significantly higher diversities within high-density species.
Three bar charts showing observed heterozygosity (==genetic diversity) over time in greater bilby (M. lagotis) populations. Panel A (Barna Mia) shows a small increase from 2003 to 2005. Panel B (Dryandra) is relatively stable within the time range between 1999 and 2005 with no clear long-term trend. Panel C (Scotia) shows a steady decline in genetic diversity from 2008 to 2016, indicating loss of variation over time.
Time-calibrated phylogenetic tree of bandicoots and bilbies (Peramelemorphia) showing evolutionary relationships and divergence times over ~60 million years. The x-axis represents time in millions of years. Major lineages, including the bilby (Macrotis lagotis) and the extinct pig-footed bandicoot (Chaeropus ecaudatus), branch off early from other bandicoots. Numerous species of bandicoots from Australia and New Guinea are shown on the right, with horizontal blue bars at nodes of the phylogeny indicating confidence intervals for estimated divergence times.
Mitochondrial genome phylogeny of cetaceans, show the Baiji is more closely related to the South American river dolphins, and then to the Narwhal and the dolphins and porpuses, than to the Susu or Ganges river dolphin.
"Majority Clade Credibility tree results from the partitioned Bayesian analyses of the concatenated data set (cytochrome b, MB, ODC) calibrated using three fossils. Numbers close to the nodes refer to maximum likelihood bootstrap support/concatenated beast posterior probabilities/species tree posterior probabilities. Values are indicated when at least one the three values was ≥70%, ≥0.95 or ≥0.95, respectively."
Best maximum-likelihood tree produced by RAxML from cyt b, ND2, and ATP6/8 sequences for six shrike taxa. Bootstrapsupport values from a 100-replicate bootstrap are included at the nodes, if above 50%.
Probabilistic population structure under the Admixed model for 236 bearded vultures Gypaetus barbatus collected from across the global distribution of the species. Individuals are sorted into four broad geographically delineated regions, and are represented by vertical lines partitioned into coloured segments which represent the estimated membership coefficients (Q-value) of each cluster represented in their genetics. ∆K = 3 was estimated as the optimal partitioning strategy
Stairway plots for estimated changes in effective population size (Ne) for A: All Cryptotis parvus parvus west of the Mississippi River excluding samples from Chaves County, and B: All Chaves County individuals. Axes are shown as logarithmic. Red lines show change in median effective population size through time, dark shading is the 75% confidence interval and light shading is the 95% confidence interval on effective size estimates.
Map of the study area. Shaded regions represent the estimated range of Cryptotis parvus, based on Hall (1981; dark shading) and Barnes and Hoffman (2023; light shading), the latter suggestive of recent westward range expansion. Filled dots represent specimens sampled for genetic analyses and are colored and labeled according to genomic cluster assignments from the SNP admixture analysis (Figure 2). Within C. parvus, samples of C. p. floridanus within Florida are colored blue (cluster 4). Other species include C. berlandieri (cluster 3) from southern Texas colored dark green, and C. soricinus (cluster 5) from Mexico colored black. Small dots show specimen localities that were not included in genomic analyses, and are only colored if clade assignment was unambiguous from the mtDNA phylogeny. Localities with black stars show specimens that have a signal of mito-nuclear discordance. Inset map provides additional spatial details for peripheral populations within New Mexico. --- photo: https://www.mammaldiversity.org/taxon/1004165/
Fig. 1. (A) The evolutionary tree of mammals depicting relationships among species that have been sequenced for the α1 subunit of the nicotinic acetylcholine receptor gene (CHRNA1). The two trees are topologically identical; ancestral-state reconstructions of amino-acid sites 187 (left-hand tree) and 189 (right-hand tree) are indicated with colored branches (legend upper left). The derived amino acid is given at the branch terminus for species that differ from the ancestral condition (tryptophan and phenylalanine for sites 187 and 189, respectively). Species that are known to survive envenomation by elapid snakes (honey badger, mongoose, hedgehog) or have been shown experimentally to have lost (mongoose, hedgehog) binding between α-bungarotoxin and the nAChR receptor are shown in red; the reduced binding ability of human is indicated with an asterisk. (B) Alignment of the α-bungarotoxin-binding region of nAChR (Barchan et al., 1995) for the 11 mammal species that have lost one or both ancestral aromatic residues at sites 187 and 189. The reconstructed ancestral placental sequence is shown for reference as is the sequence from cobra. Dots indicate sequence identity with this ancestral sequence. (C) Molecular model (Dellisanti et al., 2007a, Dellisanti et al., 2007b; UniProt Accession 2QC1) of the α1 subunit of the nicotinic acetylcholine receptor (spacefill model) shown binding with α-bungarotoxin (green ribbon model). Sites 187 and 189 are shown as the ancestral amino acid for placental mammals.
Venn diagram of Gingko genes expressed uniquely in leafs (14679), uniquely in ovules (6310), or expressed in both (42149).
Genes with differences in copy number between polar bears and brown bears. (Lower panel) VST values, which estimate the proportion of population-level copy number variation due to differences between subpopulations in copy number variation, for all 21,142 genes in the polar bear genome. Dots are colored such that red dots correspond to genes with VST > 0.35 in two methods for copy number estimation, purple dots correspond to genes with VST <= 0.35 and VST > 0.22 in two methods for copy number estimation, blue dots correspond to VST > 0.22 in one method for copy number estimation and VST > 0.35 in the second method, and gray dots correspond to VST <= 0.22 in one or both copy number estimation methods. (Upper panel) Heat map of diploid gene copy number for genes (columns) whose copy number is highly differentiated between polar bears and brown bears (n=197 genes). Each row corresponds to individual polar bears (top set of rows), brown bears (middle set of rows), and black bears (bottom set of rows). Yellow corresponds to high copy number and black corresponds to a copy number of 0.
Venn diagram depicting the numbers of shared and unique edit sites in three gymnosperm groups, Cycas, Ginkgo, and Welwitschia
Fig. 2 from Chiou et al. (2022) a, Apart from geladas, the papionin clade exhibits an extremely conserved karyotype of 42 diploid chromosomes. Twenty species with known karyotypes sampled by Stanyon et al.24 are shown with the consensus chronogram from TimeTree53,54. b, Hi-C contact map reveals a distinct lack of contacts between the arms of chromosome 7 in the reference gelada female. c, G-banded karyotyping and analysis of genomic rearrangements reveal strong synteny between fissioned chromosomes and the intact arms of chromosome 7 in central geladas and baboons, respectively. d, STRUCTURE-style bar plot showing ancestry proportions from 70 resequenced gelada genomes reveals two main populations differentiating northern (orange) and central (green) geladas. Zoo animals are of mainly central ancestry but two individuals with the highest levels of northern ancestry are also heterozygous for the centric fission characteristic of northern geladas.
Figure 5b from Caldon et al. (2005) CNVs and amylase gene copy number. (b) Normalised genomic coverage over the two loci annotated as pancreatic amylase in geladas. Arrow added to point to the increased copy number of one (LOC112607926) of the two pancreatic amylase genes in southern geladas.
a) Sliding window heterozygosity (black dots) and called ROH (runs of homozygosity) across a single scaffold for 3 pumas from 3 different populations (Big Cypress, Yellowstone, and Brazil) b) Average genome-wide heterozygosity versus the proportion of the genome in ROH c) Distribution of lengths of ROH. d) Heat map showing the percent of the genomes that are in ROH that are shared IBD (identity by descent) between pairs of pumas.
Maximum parsimony network of 32 mitochondrial control region haplotypes in American white pelicans (Pelecanus erythrorhynchos). The size of the circle is proportional to the frequency of the haplotype in the population; shading indicates the region in which the haplotype occurs (east, dark gray; west, light gray; south, white).
This phylogeny maps whole genome duplications across animals, hinting at shared ancestry with arachnids like spiders and scorpions. The images showcase Carcinoscorpius rotundicauda and Tachypleus tridentatus, two species with assembled genomes helping scientists decode their ancient genomic history.
Approximate distributions of the world’s pelican species and their respective phylogenetic relationships.
Population trajectories among four distinct Platypus population groups in Australia and Tazmania. Each group has its own trajectory, but all reach their lowest numbers of individuals at the present ime.
Evolution of autosomal chromosomes among mammal groups. From a reconstructed 60 chromosomes in the ancestral mammals to 52 in monotremes, 46 in humans, 14 in Tazmanian Devils and 18 in Opposums. Conversely, X chromosomes in marsupials and placental mammals share a common origin but monotremes instead present 5 unique X chromosomes.
Map showing the distribution pattern of two subspecies and their intergradation zone in southern Thailand. Bayesian phylogeny on mtCOI with posterior probability and bootstrap value by NJ analysis are superimposed with each node. Plastron pattern of three morphological forms of M. emys shows with respective clades.