Hydrobiologia, Journal Year: 2024, Volume and Issue: unknown
Published: Nov. 28, 2024
Language: Английский
Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(4)
Published: April 1, 2022
Abstract Cichlid fishes have repeatedly evolved an astounding diversity of trophic morphologies. For example, hypertrophied lips multiple times in both African and Neotropical cichlids could even convergently within single species assemblages such as Lake Malawi cichlids. However, the extremely high diversification rate extensive potential for hybridization has cast doubt on whether genome-level phylogenetic reconstructions delineate if these types adaptations once or times. To examine evolution this iconic trait using protein-coding noncoding nucleotide polymorphisms (SNPs), we analyzed genomes 86 cichlid species, including 33 de novo resequenced genomes. Surprisingly, genome-wide SNPs exhibited enough informativeness to reconstruct interspecific intraspecific relationships lip cichlids, although provided better support. thinning indicated most discrepancies come from relatively smaller number sites not fundamental differences their informativeness. Both coding showed that several “sand-dwelling” sampled intraspecifically, form a clade interspersed with few other nonhypertrophied lineages. We also recovered Abactochromis labrosus rock-dwelling “mbuna” lineage, starkly contrasting affinities taxa found largely sand-dwelling “nonmbuna” component radiation. Comparative analyses coupled tests introgression indicate there is no widespread between lineages taken together suggest phenotype likely at least twice independently within-lake Malawi.
Language: Английский
Citations
18
The American Naturalist, Journal Year: 2024, Volume and Issue: 204(3), P. 242 - 257
Published: May 17, 2024
AbstractAdaptive radiations highlight the mechanisms by which species and traits diversify extent to these patterns are predictable. We used 1,110 high-speed videos of suction feeding study functional morphological diversification in 300 cichlid from three African Great Lake varying ages (Victoria, Malawi, Tanganyika) an older, spatially dispersed continental radiation Neotropics. Among radiations, standing diversity was reflective time. Morphological variance Victoria, youngest radiation, a subset that within itself nested older Tanganyikan radiation. However, Neotropical cichlids often lower than Tanganyika, despite being much older. These two broadly overlapped, but each diversified into novel trait spaces not found lake radiations. Evolutionary rates across were inversely related age, suggesting extremely rapid evolution at early stages, particularly Despite this support for bursts, other inconsistent with expectations adaptive This work suggests has played out strikingly similar fashion different contingencies eventually resulting lineage-specific novelties.
Language: Английский
Citations
3
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown
Published: Oct. 6, 2023
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference tree life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, current practice leaves out large chunks genomes. As more high-quality genomes become available, we urgently need methods infer directly from a multiple genome alignment. Here, introduce CASTER, site-based method that eliminates predefine recombination-free loci. CASTER is statistically consistent under incomplete lineage sorting scalable hundreds mammalian whole We show both in simulations on real its per-site scores can reveal interesting patterns evolution across genome.
Language: Английский
Citations
8
Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(5)
Published: May 1, 2023
Abstract The genomic loci generating both adaptive and maladaptive variation could be surprisingly predictable in deeply homologous vertebrate structures like the lips. Variation highly conserved traits such as jaws teeth organisms evolutionarily disparate teleost fishes mammals is known to structured by same genes. Likewise, hypertrophied lips that have evolved repeatedly Neotropical African cichlid fish lineages share unexpectedly similar genetic bases themselves even provide surprising insight into underlying human craniofacial anomalies. To isolate regions divergence lips, we first employed genome-wide associations (GWAs) several species of cichlids from Lake Malawi. Then, tested if these GWA were shared through hybridization with another Malawi lineage has seemingly parallel. Overall, introgression among lip appeared limited. Among our regions, one contained gene kcnj2 been implicated convergently Central American Midas diverged radiation over 50 million years ago. also additional genes cause lip–associated birth defects. Cichlid are becoming prominent examples replicated architecture trait convergence increasingly providing anomalies a cleft lip.
Language: Английский
Citations
7
Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 202, P. 108222 - 108222
Published: Oct. 30, 2024
Language: Английский
Citations
2
Genomics, Journal Year: 2023, Volume and Issue: 116(1), P. 110771 - 110771
Published: Dec. 24, 2023
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of most species-rich shark order, Carcharhiniformes (ground sharks) has led to challenges phylogenomic reconstruction families and genera belonging particularly family Triakidae (houndsharks). current state phylogeny remains controversial, with arguments for both monophyly paraphyly within family. We hypothesize that this variability is triggered by selection different a priori partitioning schemes account site gene heterogeneity mitogenome. Here we used an extensive statistical framework select scheme inference relationships Carcharhiniformes, tested heterogeneous CAT + GTR G4 models incorporated multi-species coalescent model (MSCM) into our analyses influence tree discordance on species inference. included five newly assembled houndshark mitogenomes increase resolution Triakidae. During assembly procedure, uncovered 714 bp-duplication mitogenome Galeorhinus galeus. Phylogenetic confirmed existence two distinct clades expanded Mustelus genus. latter alludes potential reversal reproductive mode from placental aplacental, suggesting played role trajectory adaptive divergence. These new sequences have contribute population genomic investigations, phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies these ecologically economically important species.
Language: Английский
Citations
6
Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 40(1)
Published: Dec. 22, 2022
Abstract Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai–Tibetan Plateau (QHTP) its vicinity have been reduced residual movement climatic zones during Pleistocene recent anthropogenic disturbance, whereas plateau pika (O. curzoniae) remains common. Population-level whole-genome sequencing (n = 142) six closely related subgenus Ochotona revealed several phases ancient introgression, lineage replacement, bidirectional introgression. The strength was greatest dominant O. curzoniae ecologically distinct areas peripheral QHTP. Genetic analyses were consistent environmental reconstructions past population movements. Recurrent periods introgression throughout an increase variation at first subsequent loss later phases. Enhanced dispersion introgressed genomic regions apparently contributed demographic recovery three underwent range shifts following climate oscillations on QHTP, although it failed drive northeastern dauurica isolated sikimaria. Our findings highlight differences timescale background determine consequence unique role QHTP conserving key evolutionary processes sky island species.
Language: Английский
Citations
9
Taxon, Journal Year: 2023, Volume and Issue: 72(4), P. 724 - 732
Published: June 1, 2023
Abstract Comparative morphology was for many years the main source of information systematic studies. As a result molecular revolution in evolutionary botanical research early 1990s, we can now rely on system classification based primarily or exclusively DNA. Nevertheless, would like to emphasise importance this era phylogenetics. We argue that comparative morphology, using latest technologies and developmental studies, is modern important scientific discipline essential better understand evolution angiosperms other taxa. This paper also offers guideline emerging morphologists phylogeneticists aiming include their research.
Language: Английский
Citations
5
Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 190, P. 107965 - 107965
Published: Nov. 16, 2023
Language: Английский
Citations
5
bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown
Published: April 28, 2024
Abstract Fish is an important source of animal protein for many people living around Lake Malawi. The evaluation population structure and genetic diversity can yield useful information management conservation fish species but complicated in Malawi by the close relatedness recent cichlid adaptive radiation. In this study, we analysed whole-genome sequencing data “true utaka”, a group cichlids previously common fisheries, that has faced strong decline due to overfishing. Our analysis 223 individuals collected from fishermen’s catches along western shoreline confirmed Copadichromis mloto ( C. sp . “virginalis kajose”) true utaka most targeted fisheries. Genetic principal component analysis, phylogenetic inference, admixture revealed complex patterns structure. presence at least three geographically widespread clades have remained separate despite gene flow partial sympatry hints currently undescribed, cryptic This result leads us suggest that, lack obvious habitat barriers, benthic pelagic might harbour unidentified calls further taxonomic research define appropriate units.
Language: Английский
Citations
1