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opencc-by-4.0Oct 2023View details →

Genetic variability among and within domestic Old and New World Camels at the α-lactalbumin gene (LALBA) reveals new alleles and polymorphisms responsible for differential expression

Supplementary Figure 1. Schematic representation of the LALBA gene in camelids. Boxes indicate the exons (black for the un-translated, white for the signal peptide and grey for the translated). The line shows introns, 5’- and 3’-flanking regions. Supplementary Figure 2. Alignment of the α-LA calcium-binding site (red rectangle) of 23 terrestrial species available in the UniProt database (<a href="http://www.uniprot.org/uniprot/">http://www.uniprot.org/uniprot/</a>). The calcium-binding site in the Camelus dromedarius is indicated by a yellow rectangle.

opencc-zeroDec 2023View details →

Genetic and behavioral factors affecting interpopulation color pattern variation in two congeneric chameleon species

We conducted a study on interpopulation variation of color patterns in two congeneric chameleon species, which have an analogous life history. Both species are able to rapidly change color pattern, and context-dependent color patterns often vary across a wide geographic range. Specifically, we tested four hypotheses that can explain the observed interpopulation variation of color patterns by a series of behavioral field trials where the color patterns of individuals were recorded and later analyzed by a deep neural network algorithm. We used redundancy analysis (dbRDA) to relate genetic, spectral, and behavioral predictors to interpopulation color pattern distance. Our results showed that both isolation by distance and alternative mating tactics were significant predictors for interpopulation color pattern variation in Chamaeleo chamaeleon males. In contrast, in C. dilepis, the interpopulation color pattern variation was largely explained by isolation by distance, and the evidence for alternative mating tactics was absent. In both chameleon species, the environmental colors showed no evidence of influencing chameleon interpopulation color pattern variation, regardless of sex or behavioral context. This contrasting finding suggests that interpopulation context-dependent color pattern variations in each species are maintained under a different set of selective pressures or circumstances.

opencc-zeroJan 2024View details →

Data from: The twenty amino acids are identified by unique numbers assigned to the uracil, cytosine, adenine, and guanine found in the three base positions of the sixty-four messenger RNA genetic codons

A codon's three bases consist of any combination of uracil, cytosine, adenine, or guanine and these encode the twenty amino acids. When the codon's first two bases are given specific values, and those values are multiplied, then the third base of the codon is used during translation only when the product is greater than three. Here we show that those values plus more variables within the ribosomal decoding site results in specific flow values for each of the twenty amino acid groups. These results are demonstrated in a flow chart showing the unidirectional flow which is expected during the translation process. All twenty amino acids can be represented by numbers that describe their relationship to each other and to the decoding site. We anticipate our findings will increase discussion about using a number system to better understand the translation process.

opencc-zeroJan 2024View details →

The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution

The Pacific harbor seal (Phoca vitulina richardii) occurs in the Mexican Pacific region at the southernmost edge of the subspecies' distribution, along 700 km of coastline and on nine islands west of the Baja California peninsula. Its abundance corresponds to 3% of its total abundance in the north Pacific Ocean. The species is considered relatively sedentary and highly philopatric, which make it vulnerable to stochastic processes; thus, reproductive and genetic isolation of the Mexican Pacific colonies is expected. This study aimed to genetically characterize the harbor seal in the Mexican Pacific to inform conservation efforts. We estimated the levels of genetic diversity for five colonies, using a 572-base pair mitochondrial DNA control region fragment and nine microsatellite loci. We examined the population genetic structure and its phylogeographic patterns. We found 15 variable sites that defined 18 mitochondrial DNA haplotypes. Results show one of the lowest levels of diversity reported for the species (overall haplotype diversity h = 0.626 ± SD 0.041; overall nucleotide diversity π = 0.0018 ± SD 0.0013; mean expected heterozygosity HE = 0.537). We found a stronger genetic structure with both markers than in the larger regions of the north Pacific, from Alaska to California. The Pacific harbor seal colonies found in Mexico may have their origins in northern colonies, via a founder event. We found only four haplotypes in common with those observed (451) along the rest of the Pacific colonies, while nine of the 14 haplotypes exclusive to the Mexican Pacific are private.

opencc-by-4.0Sep 2023View details →

Dataset from: Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure

Genetic variation of the entire genome represents population structure, yet individual loci can show distinct patterns. Such deviations identified through genome scans have often been attributed to effects of selection instead of randomness. This interpretation assumes that long enough genomic intervals average out randomness in underlying genealogies, which represent local genetic ancestries. However, an alternative explanation to distinct patterns has not been fully addressed: too few genealogies to average out the effect of randomness. Specifically, distinct patterns of genetic variation may be due to reduced local recombination rate, which reduces the number of genealogies in a genomic window. Here, we associate distinct patterns of local genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using genome sequences and recombination maps. We find that distinct patterns of local genetic variation reflect haplotype structure at low-recombining regions either shared in most populations or found only in a few populations. At the former species-wide low-recombining regions, genetic variation depicts conspicuous haplotypes segregating in multiple populations. At the latter population-specific low-recombining regions, genetic variation represents variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns of haplotype structure evolve due to reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolution of reduced local recombination rate. Recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.

opencc-zeroFeb 2024View details →

Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)

Obovaria olivaria is a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions. Obovaria olivaria uses the similarly imperiled Acipenser fulvescens (Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to assess patterns of genetic diversity and population structure of O. olivaria from 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. Pairwise FST ranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure of O. olivaria is consistent with the existing literature on Acipenser fulvescens and suggest that, although northern and southern O. olivaria populations are genetically distinct, genetic structure in O. olivaria is largely clinal rather than discrete across its range. Conservation and restoration efforts of O. olivaria should prioritize the maintenance and restoration of locations where O. olivaria remain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal of Acipenser fulvescens and movement of encysted glochidia.

Fig. 1. Colonial ISoxYa manangona n in Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya,

Fig. 1. Colonial ISoxYa manangona n. sp. from Andasibe, Madagascar. (a) A part of a colony with 79 spiders in 41 webs (image shows 23 webs). (b) A detail from another colony where females are in their individual webs (image shows 14 of the 16 webs in the colony) while males hang on line in between webs (image shows 12 males). (c) A detail of another colony showing male leks.These males showed no overt intrasexual aggression that would be typical of solitary spiders.

Fig. 26 in Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya,

Fig. 26. Clustering of individuals from the nine web colonies (A–I) based on discriminant analysis of principal components from unlinked SNPs.

Plate 2. Figs. 9–17 in Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya,

Plate 2. Figs. 9–17. Male: dorsal (Fig. 9), ventral (Fig. 10), side (Fig. 11); palp: dorsal (Fig. 12), ventral (Fig. 13), retrolateral (Fig. 14), prolateral (Fig. 15); line drawings: dorsal palp (Fig. 16), median apophysis (Fig. 17).

Plate 3. Figs. 18–25 in Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya,

Plate 3. Figs. 18–25. Female: melanic dorsal (Fig. 18), ventral (Fig. 19); light dorsal (Fig. 20), ventral (Fig. 21); Male: melanic dorsal (Fig. 22), ventral (Fig. 23); light dorsal (Fig. 24), ventral (Fig. 25).

Fig. 28 in Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya,

Fig. 28. Unsupervised machine learning clustering analysis based on unlinked SNPs using variational autoencoders. Colors for individuals are based on the web colony (A–I) from which they were collected.

Plate 1. Figs. 2–8 in Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya,

Plate 1. Figs. 2–8. Female: dorsal (Fig. 2), ventral (Fig. 3), side (Fig. 4); epigyne: ventral (Fig 5), posterior (Fig. 6), spermatheca dorsal (Fig. 7); line drawing: epigyne ventral (Fig. 8).

Fig. 27 in Discovery and Genetic Characterization of Single Cohort Adult Colonies With Male Aggregations, and Preliminary Evidence for Lekking in a Malagasy Kite Spider (Isoxya,

Fig. 27. Membership probability for each individual to the nine web colonies (A–I) based on the discriminant analysis of principal components clustering from unlinked SNPs.

FIGURE 7 in Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

FIGURE 7. View of the ventrum of three individuals of Chaerephon atsinanana sp. nov. captured the same day and from the same colony at Andasibe, showing the range of variation in ventrum coloration (left to right): Male (FMNH 184504, RHF 068), female (FMNH 184506, RHF 070), and female (FMNH 184508, RHF 072).

FIGURE 6 in Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

FIGURE 6. Lateral view of central portion of external right ear and antitragus of different Chaerephon spp.: A – C. atsinanana sp. nov. (FMNH 188144) from Madagascar: Province de Toamasina, Commune Anjiro, Marozevo; B – C. leucogaster (FMNH 188644) from Madagascar: Province d'Antsiranana, Nosy Komba, Ampangorinana; C – C. pumilus sensu stricto (BMNH 19.7.7.334) from Massawa, Eritrea, the type locality of this taxon.

FIGURE 3 in Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

FIGURE 3. Different views of skull and mandible of an adult female C. 'pumilus' (eastern Madagascar, described herein as Chaerephon atsinanana sp. nov.) (left set - FMNH 185259, holotype, GSL = 17.0 mm) obtained at Farafangana; adult female C. pumilus sensu stricto (middle set - USNM 38032, GSL = 15.9 mm) collected at Massawa, Eritrea, which is the type locality of this species; and adult female C. leucogaster (right set - FMNH 185228, GSL = 15.4 mm) obtained from Manakara: upper row, dorsal and ventral views of crania and lower row pair, lateral view of crania and mandibles. Arrows indicate differences between the three taxa in the M3 hypoconal flange. (Photograph taken by John Weinstein, FMNH image.)

FIGURE 2 in Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

FIGURE 2. Dendrogram based on analyses of 206 nucleotides of the mitochondrial cytochrome b gene illustrating relationships between Chaerephon pumilus from the type locality of Massawa, Eritrea, and other Chaerephon clades: C. pumilus sensu lato (Tanzania), C. pumilus sensu stricto (Yemen), C. leucogaster (western Madagascar), C. pusillus (Aldabra), and C. 'pumilus' (eastern Madagascar, described herein as C. atsinanana sp. nov.). All sequenced individuals belonging to the above-mentioned taxa clustered into monophlyletic groups. Chaerephon chapini from mainland Africa, Mops leucostigma, and M. midas are used as outgroups. Nodal support is indicated according to the following analyses: Bayesian posterior probability in standard font (top), bootstrap value (1000 pseudo-replicates) for maximum parsimony analysis in bold font (middle), and neighbor-joining analysis underlined (bottom). Bootstrap values of less than 50% and posterior probabilities of less than 0.7 are not indicated.

FIGURE 1 in Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

FIGURE 1. Distribution of Chaerephon 'pumilus' (described herein as C. atsinanana sp. nov.). Map to the left is of the eastern portion of Africa, the Comoros Archipelago, Aldabra, and Madagascar. The larger map to the right of Madagascar illustrates known collection localities of specimens of C. atsinanana (eastern Madagascar) and C. leucogaster. The two species occur in sympatry at Manakara.

FIGURE 5 in Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

FIGURE 5. Tree based on analyses of 332 nucleotides of the mitochondrial D-loop illustrating relationships between 40 haplotypes of Chaerephon spp. with respect to the outgroup M. midas from Madagascar (haplotype 41). Nodal support is indicated according to the following analyses used: Bayesian posterior probability in standard font (top), bootstrap value (1000 pseudo-replicates) for maximum parsimony analysis in bold font (middle), and neighbor-joining analysis underlined (bottom). Bootstrap values of less than 50% and posterior probabilities of less than 0.7 are not indicated. Clade designations A, B, C2a, and C2b match those in Fig. 6. Chaerephon 'pumilus' from eastern Madagascar is described herein as C. atsinanana sp. nov.

FIGURE 4 in Patterns of morphological and genetic variation in western Indian Ocean members of the Chaerephon 'pumilus' complex (Chiroptera: Molossidae), with the description of a new species from Madagascar

FIGURE 4. Tree based on analyses of 1031 nucleotides of the mitochondrial cytochrome b gene illustrating relationships between 20 haplotypes of Chaerephon spp. with respect to the outgroups Mops leucostigma from Madagascar (haplotypes 22 and 23), M. midas from Madagascar (haplotype 21), and Otomops martiensseni from Kenya (haplotype 24). Nodal support is indicated according to the following analyses used: Bayesian posterior probability in standard font (top), bootstrap value (1000 pseudo-replicates) for maximum parsimony analysis in bold font (middle), and neighbor-joining analysis underlined (bottom). Bootstrap values of less than 50% and posterior probabilities of less than 0.7 are not indicated. Chaerephon 'pumilus' from eastern Madagascar is described herein as C. atsinanana sp. nov.