Molecular Phylogenetics and Evolution最新文献

With 289 known species in 51 genera, the ophidiiform family Ophidiidae together with their relatives from the Carapidae (36 species in eight genera) of the same suborder Ophidioidei dominate the deep sea, but some occur also in shallow water habitats. Despite their high species diversity in the deep sea and wide bathymetric distributions, their phylogenetic relationships and evolution remain unexplored due in part to sampling difficulties. Thanks to the biodiversity exploratory program entitled “Tropical Deep-Sea Benthos” and joint efforts between Taiwan and French teams for sampling from different localities across the Indo-West Pacific over the last two decades, we are able to compile comprehensive datasets for investigations. In this study, 59 samples representing 36 of 59 known ophidioid genera are selected and used to construct a multi-gene dataset to infer the phylogenetic relationships of ophidioid fishes and their relatives. Our results reveal that the Ophidiidae forms a paraphyletic group with respect to the Carapidae. The four main clades of Ophidioidei resolved are the (1) clade comprising species from the subfamily Brotulinae; (2) clade that includes species in the genera Acanthonus and Xyelacyba; (3) clade grouping Hypopleuron caninum with species from the family Carapidae; and (4) clade containing the species in the subfamily Brotulotaenilinae, Neobythitinae (in part), and Ophidiinae. Accordingly, we suggest the following new revisions based on our results and proposed morphological diagnoses. The subfamily Brotulinae should be elevated to the family level. The genera Xyelacyba and probably Tauredophidium (unsampled in this study) should be included in the newly established family Acanthonidae with Acanthonus. The families Carapidae and Ophidiidae are re-defined. Our time-calibrated phylogenetic and ancestral depth reconstructions enable us to clarify the evolutionary history of ophidiiform fishes and infer past patterns of species distributions at different depths. While Ophidiiformes is inferred to have originated in shallow waters around 96.25 million years ago (Mya), the common ancestor to the Ophidioidei is inferred to have invaded the deep sea around 90.22 Mya, the dates coinciding with the global anoxic event of the OAE2. The observed bathymetric distribution patterns in Ophidioidei most likely point to the mesopelagic zone as the center of origin and diversification. This was followed by multiple events of depth transitions or range expansions towards either shallower waters or greater depth zones, which were likely triggered by past climate changes during the Paleogene-Neogene.

Subterranean rodents of the genus Ctenomys (tuco-tucos) are endemic to South America and have experienced relatively recent radiation. There are about 67 recognized species that originated in approximately 1–2 MY. They stand out for their species richness, extraordinary chromosomal diversity, and wide range of habitat they occupy in the continent. Phylogenetic relationships among species of tuco-tucos have been challenging to resolve. Groups of closely-related species have been suggested, but their relationships must be resolved. This study estimates the phylogeny of the genus using massive sequencing, generating thousands of independent molecular markers obtained by RADseq, with a taxonomic sampling that includes 66% of the recognized species. The sequences obtained were mapped against the C. sociabilis genome, recovering up to 1,215 widely shared RAD loci with more than 19,000 polymorphic sites. Our new phylogenetic hypothesis corroborated the species groups previously proposed with cytochrome b gene sequences and provided a much greater resolution of the relationships among species groups. The frater group is sister to all other tuco-tucos, whereas some of the earlierliest proposals placed the sociabilis group as sister to all other tuco-tucos. Ctenomys leucodon, previously proposed as an independent lineage, is associated with the frater group with moderate statistical support. The magellanicus and mendocinus are sister groups in a major clade formed by the boliviensis, talarum, tucumanus, torquatus, and opimus groups. Ctenomys viperinus, included in the phylogeny for the first time, belongs to the tucumanus group. This multi-locus phylogenetic hypothesis provides insights into the historical biogeography of understanding this highly diverse genus.

The Salicaceae includes approximately 54 genera and over 1,400 species with a cosmopolitan distribution. Members of the family are well-known for their diverse secondary plant metabolites, and they play crucial roles in tropical and temperate forest ecosystems. Phylogenetic reconstruction of the Salicaceae has been historically challenging due to the limitations of molecular markers and the extensive history of hybridization and polyploidy within the family. Our study employs whole-genome sequencing of 74 species to generate an extensive phylogeny of the Salicaceae. We generated two RAD-Seq enriched whole-genome sequence datasets and extracted two additional gene sets corresponding to the universal Angiosperms353 and Salicaceae-specific targeted-capture arrays. We reconstructed maximum likelihood-based molecular phylogenies using supermatrix and coalescent-based supertree approaches. Our fossil-calibrated phylogeny estimates that the Salicaceae originated around 128 million years ago and unravels the complex taxonomic relationships within the family. Our findings confirm the non-monophyly of the subgenus Salix s.l. and further support the merging of subgenera Chamaetia and Vetrix, both of which exhibit intricate patterns within and among different sections. Overall, our study not only enhances our understanding of the evolution of the Salicaceae, but also provides valuable insights into the complex relationships within the family.

Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.

Gadopsis (Percichthyidae) is a freshwater genus distributed in south-eastern Australia, including Tasmania, and comprises two recognized species. Previous molecular phylogenetic investigations of the genus, mostly conducted in the pre-genomics era and reflecting a range of geographic and molecular sampling intensities, have supported the recognition of up to seven candidate species. Here we analyze a genome-wide SNP dataset that provides comprehensive geographic and genomic coverage of Gadopsis to produce a robust hypothesis of species boundaries and evolutionary relationships. We then leverage the SNP dataset to characterize relationships within candidate species that lack clear intraspecific phylogenetic relationships. We find further support for the seven previously identified candidate species of Gadopsis and evidence that the Bass Strait centered candidate species (SBA) originated from ancient hybridization. The SNP dataset permits a high degree of intraspecific resolution, providing improvements over previous studies, with numerous candidate species showing intraspecific divisions in phylogenetic analysis. Further population genetic analysis of the Murray-Darling candidate species (NMD) and SBA finds support for K = 6 and K = 7 genetic clusters, respectively. The SNP data generated for this study have diverse applications in natural resource management for these fishes of conservation concern.

Incomplete Lineage Sorting (ILS) and introgression are among the two main factors causing incongruence between gene and species trees. Advances in phylogenomic studies have allowed us to overcome most of these issues, providing reliable phylogenetic hypotheses while revealing the underlying evolutionary scenario. Across the last century, many incongruent phylogenetic reconstructions were recovered for Drosophilidae, employing a limited sampling of genetic markers or species. In these studies, the monophyly and the phylogenetic positioning of the Zygothrica genus group stood out as one of the most controversial questions. Thus, here, we addressed these issues using a phylogenomic approach, while accessing the influence of ILS and introgressions on the diversification of these species and addressing the spatio-temporal scenario associated with their evolution. For this task, the genomes of nine specimens from six Neotropical species belonging to the Zygothrica genus group were sequenced and evaluated in a phylogenetic framework encompassing other 39 species of Drosophilidae. Nucleotide and amino acid sequences recovered for a set of 2,534 single-copy genes by BUSCO were employed to reconstruct maximum likelihood (ML) concatenated and multi-species coalescent (MSC) trees. Likelihood mapping, quartet sampling, and reticulation tests were employed to infer the level and causes of incongruence. Lastly, a penalized-likelihood molecular clock strategy with fossil calibrations was performed to infer divergence times. Taken together, our results recovered the subdivision of Drosophila into six different lineages, one of which clusters species of the Zygothrica genus group (except for H. duncani). The divergence of this lineage was dated to Oligocene ∼ 31 Mya and seems to have occurred in the same timeframe as other key diversification within Drosophila. According to the concatenated and MSC strategies, this lineage is sister to the clade joining Drosophila (Siphlodora) with the Hawaiian Drosophila and Scaptomyza. Likelihood mapping, quartet sampling, reticulation reconstructions as well as introgression tests revealed that this lineage was the target of several hybridization events involving the ancestors of different Drosophila lineages. Thus, our results generally show introgression as a major source of previous incongruence. Nevertheless, the similar diversification times recovered for several of the Neotropical Drosophila lineages also support the scenario of multiple and simultaneous diversifications taking place at the base of Drosophilidae phylogeny, at least in the Neotropics.

Recent advances in sequencing technology and phylogenetic methods allow us to solve puzzling taxonomic questions using detailed analyses of genetic diversity of populations and gene flow between them. The genus of solitary-living dune mole-rat, Bathyergus, is quite unique among six genera of African mole-rats. The animals are by far the largest and the only scratch digging mole-rat genus possessing a skull less adapted to digging, grooved upper incisors, and more surface locomotor activity. Most authors recognize two species of dune mole-rats, B. suillus and B. janetta, but according to others, the genus is monotypic. In addition, recent molecular studies have revealed cryptic genetic diversity and suggested the existence of up to four species. In our study, we used mitochondrial and genome-wide nuclear data collected throughout the distribution of the genus to investigate the number of species. In agreement with previous studies, we found Bathyergus to be differentiated into several distinct lineages, but we also found evidence for a degree of gene flow between some of them. Furthermore, we confirmed that B. janetta is nested within B. suillus, making the latter paraphyletic and we documented an instance of local mitochondrial introgression between these two nominal species. Phylogeographic structure of the genus was found to be very shallow. Although traditionally dated to the Miocene, we found the first split within the genus to be much younger estimated to 0.82 Ma before present. Genealogical distinctiveness of some lineages was very low, and the coancestry matrix showed extensive sharing of closely related haplotypes throughout the genus. Accordingly, Infomap clustering on the matrix showed all populations to form a single cluster. Overall, our study tends to support the existence of only one species of Bathyergus namely, B. suillus. Environmental niche modelling confirmed its dependence on sandy soils and the preference for soils with relatively high carbon content. Bayesian skyline plots indicate recent population decline in the janetta lineage, probably related to global environmental change.

The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a single phylogenetic network with the smallest possible number of reticulation nodes. This problem is computationally hard and previous solutions are limited to small and/or severely restricted data sets, for example, a set of binary trees with the same taxon set or only two non-binary trees with non-equal taxon sets. Building on our previous work on binary trees, we present FHyNCH, the first algorithmic framework to heuristically solve the Hybridization problem for large sets of multifurcating trees whose sets of taxa may differ. Our heuristics combine the cherry-picking technique, recently proposed to solve the same problem for binary trees, with two carefully designed machine-learning models. We demonstrate that our methods are practical and produce qualitatively good solutions through experiments on both synthetic and real data sets.

Hordeum is an economically and evolutionarily important genus within the Triticeae tribe of the family Poaceae, and contains 33 widely distributed and diverse species which cytologically represent four subgenomes (H, Xa, Xu and I). These wild species (except Hordeum spontaneum, which is the primary gene pool of barley) are secondary or tertiary gene-pool germplasms for barley and wheat improvement, and uncovering their complicated evolutionary relationships would benefit for future breeding programs. Here, we developed a complexity-reduced pipeline via capturing genome-wide distributed fragments via two novel target-enriched assays (HorCap v1.0 and BarPlex v1.0) in conjugation with high-throughput sequencing of the enrichments. Both assays were tested for genotyping 40 species from three genera (Hordeum, Triticum, and Aegilops) containing 82 samples 67 accessions. Either of both assays worked efficiently in genotyping, while integration of both assays can significantly improve the robustness and resolution of the Hordeum phylogenetic trees. Interestingly, the incomplete lineage sorting (ILS) was inferred for the first time as the major factor causing phylogenetic discordance among the four subgenomes, whereas in New World species (carrying I genome) post-speciation introgression events were revealed. Through revising the evolutionary relationships of the Hordeum species based on an ancestral state reconstruction for the diploids and parental donor inference for the polyploids, our results raised new queries about the Hordeum phylogeny. Moreover, both newly-developed assays are applicable in genotyping and phylogenetic analysis of Hordeum and other Triticeae wild species.