Biology subjects

Larkin, D. M.

Publications and source records attributed to Larkin, D. M..

5 recordsLinked to original sources

bioRxiv2026

MC1R residue 223 is a convergent target for coat-colour lightening in domestic and wild bovids

Whether similar phenotypes evolve through shared substitutions or alternative molecular routes is a central question in evolutionary genomics. Grey-coated taurine cattle provide a powerful system for investigating this question using geographically distinct Podolian and Alpine lineages. We combined whole-genome resequencing data, complementary selection scans (hapFLK, DCMS and FST) and contrasts between grey-coated and non-grey-coated breeds to investigate the molecular evolution of grey coat colour. Selection analyses identified candidate regions associated with Podolian/steppe divergence and a prominent pigmentation-related signal on BTA18 contaning FANCA, MC1R, and SPIRE2. Most grey breeds shared a BTA18 haplotype containing MC1R p.Arg223Trp and additional candidate variants. Tyrolean Grey cattle lacked this predominant haplotype but carried the coding duplication p.Gly220_Arg223dup, together with differentiation near the ASIP regulatory region. Thus, different candidate coding changes affect the same MC1R residue in different cattle lineages. Haplotype comparisons supported independent Podolian and Alpine origins for p.Arg223Trp and p.Gly220_Arg223dup insertion, respectively. Ancient-genome screening yielded no validated evidence of either variant except p.Arg223Trp in medieval cattle. Comparisons across 1,108 mammalian taxa identified independent recurrence of p.Arg223Trp in the white-coated mountain goat, Oreamnos americanus, where the derived allele was fixed in surveyed individuals (JTT-based neutral probability = 0.0043). Our findings support a model in which grey coat colour in cattle evolved through at least two partially distinct molecular routes within interacting pigmentation pathways. More broadly, they identify MC1R residue 223 as a candidate recurrent target of coat-colour lightening and illustrate how domesticated and wild lineages can repeatedly target constrained functional positions during phenotypic evolution.

evolutionary biology↗

bioRxiv2020

Demographic history, cold adaptation, and recent NRAP recurrent convergent evolution at amino acid residue 100 in the world northernmost cattle from Russia

Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories for two of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, while Yakut cattle separated from European taurines ~5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation, H100Q, in a highly conserved NRAP gene, represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from nine distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.

genomics↗

bioRxiv2019

Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

Once recombination is halted between the X and Y chromosome, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about variation in sex chromosome differentiation within clades. Here, we combined whole genome and transcriptome sequencing data to characterise the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged 30 mya. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata are largely homomorphic, with recombination persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely non-recombining and strikingly heteromorphic. ln addition to being highly divergent, the sex chromosome system in P. picta includes a neo-sex chromosome, the result of a fusion between the ancestral sex chromosome and part of chromosome 7. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of complete dosage compensation in this species, the first such documented case in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

evolutionary biology↗

bioRxiv2019

The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes

BackgroundTsetse flies (Glossina sp.) are the sole vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood specific diet by both sexes and obligate bacterial symbiosis. This work describes comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans (G.m. morsitans), G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes) and Fusca (G. brevipalpis) which represent different habitats, host preferences and vectorial capacity. ResultsGenomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex linked scaffolds show increased rates of female specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse specific genes are enriched in protease, odorant binding and helicase activities. Lactation associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other characterized insects. Vision associated Rhodopsin genes show conservation of motion detection/tracking functions and significant variance in the Rhodopsin detecting colors in the blue wavelength ranges. ConclusionsExpanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.

genomics↗

bioRxiv2018

Germline-Restricted Chromosome (GRC) is Widespread among Songbirds

The genome of flying birds, the smallest among amniotes, reflects overweight of the extensive DNA loss over the unrestricted proliferation of selfish genetic elements, resulted in a shortage of repeated sequences and lack of B-chromosomes. The only exception of this rule has been described in zebra finch, which possesses a large germ-line restricted chromosome (GRC), transmitted via oocytes, eliminated from male postmeiotic cells and absent in somatic cell. It is considered as a rarity and its origin, content and function remain unclear. We discovered that all songbirds possess GRC: in various size and genetic content it is present in all fifteen songbird species investigated and absent from germ-line genomes of all eight species of other bird orders examined. Our data based on fluorescent in situ hybridization of DNA probes derived from GRCs of four different Passeri species and their sequencing indicate that the GRCs show low homology between avian species. They contain fragments of the somatic genomes, which include various unique and repetitive sequences. We propose that the GRC has formed in the common ancestor of the extant songbirds and undergone subsequent divergence. GRC presence in the germ line of every songbird studied indicate that it could contain genetic element(s) indispensable for gametogenesis, which are yet to be discovered.

evolutionary biology↗