Multilocus Species Tree Research Articles

Description and comparative genome analysis of Hallella absiana sp. nov., isolated from pig feces

ObjectiveThe genus Hallella was described within Bacteroidaceae, and then reclassified within Prevotellaceae based on its phenotypic and phylogenetic description. It is associated with degradation of carbohydrate. However, some species of Hallella have pathobiotic properties, and are involved in infections and chronic inflammatory disorders. MethodsHere, we used a polyphasic taxonomic approach to characterize the two strains: YH-C38T and YH-C4B9b. A detailed metabolic analysis was conducted to compare the two novel isolates with related strains within the genus Hallella. ResultAnalysis of 16S rRNA gene sequences revealed that the isolates were most closely related to Hallella mizrahii JCM 34422T with 98.5% and 98.6% similarities, respectively. Analysis of the multi-locus species tree based on whole genome sequences of the isolates and related strains revealed that the isolates formed a sub-cluster adjacent to H. mizrahii JCM 34422T. The average nucleotide identity values for YH-C38T and YH-C4B9b, and the most closely related strain H. mizrahii JCM 34422T, were 93.5% and 93.8%, respectively. The main fatty acids were iso C17:0 3OH and anteiso C15:0. The predominant menaquinones were MK-12, MK-11, and MK-13. The cell wall contained the peptidoglycan of meso-diaminopimelic acid. Analysis of comparative metabolic analysis revealed that isolates YH-C38T and YH-C4B9b each contained 155 carbohydrate-active enzymes, and glycoside hydrolase was the largest family. ConclusionTwo rod-shaped, obligately anaerobic, Gram-stain-negative bacteria, isolated from pig feces, were designated as strains YH-C38T and YH-C4B9b. Based on the chemotaxonomic, phenotypic, and phylogenetic properties, YH-C38T (=KCTC 25103T = JCM 35423T) and YH-C4B9b (=KCTC 25104 = JCM 35609) represent a novel taxon. The name Hallella absiana sp. nov. is proposed.

A novel strain of Shigella isolated from the gut of Lepidocephalichthys guntea has in its genome a complete gene package for Type ll secretion system, and elaborate repertoire of genes responsible for multiple antibiotic-resistance and metal resistance via specific efflux channels.

The bacterial strain GCP5 was isolated from the gut of a bottom-dwelling fish Lepidocephalichthys guntea, that lives in the Magurmari River near North Bengal University in Siliguri, India. GCP5 was phylogenetically assigned to the Shigella genus using whole genome-based trees, k-mer analysis, the multilocus species tree (MLST), and single nucleotide polymorphism (SNP)-based trees, and the genetic makeup of the isolate was determined following assembly of the genome sequences and genome annotation with several bioinformatics tools. The presence of a complete package of general-secretory-pathway (gsp) genes, grouped in an operon identical to a well-characterized type II secretion system (T2SS), was confirmed by genome mining of Shigella sp. GCP5. The operon's gsp genes shared the most homology with Escherichia coli gsp genes. A few more high-pathogenicity islands (HPIs) in the GCP5 genome were validated using the pan-genomes analysis pipeline (PGAP) and island viewer. Several antibiotic-resistance genes were found in this genome, as well as the existence of key antibiotic efflux pump families, allowing for the creation of a gene network of several antibiotic efflux transporters. In addition, the genome contained genes specific for nickel transport, the nikABCD system, and the RND family transporter cusCFBA, which confers resistance to copper and silver by effluxing out Cu+ and Ag+ ions.

Paraburkholderia bengalensis sp. nov. isolated from roots of Oryza sativa, IR64.

Paraburkholderia bengalensis sp. nov. strain IR64_4_BI was isolated from rice roots cultivated in Madhyamgram field station of Bose Institute, West Bengal, India. IR64_4_BI is a Gram-negative, motile, nitrate-reducing, nitrogen-fixing bacterium. Whole-cell fatty acid analyses of IR64_4_BI show C16:0, summed feature 8 (comprising C18:1ω7c and/or C18:1 ω 6c) and summed feature 3(C16:1 w7c/C16:1 w6c or C16:1 ω 7c/C16:1 ω 6c) were the predominant fatty acids. 16S rRNA phylogeny showed that it was most similar to P. phymatum STM815T (98.5% identity), P. terrae KMY02T (98.44% identity) and P. hospita LMG 20598T (98.32% identity). The Average Nucleotide Identity-BLAST (ANIb) of P. bengalensis IR64_4_BI with P. hospita DSM 17164T, P. terrae DSM 17804T, P. phymatum STM815T and P. hospita LMG 20598T was 83.11, 83.52, 84.5 and 83.12% respectively. Comparison of genome sequence of IR64_4_BI with other species of Paraburkholderia using the Multi-locus species tree software show that P. bengalensis IR64_4_BI is a novel species. The ability of P. bengalensis IR64_4_BI to survive on nitrogen-free medium under microaerophilic conditions and the abundance of nitrogen metabolism-related genes makes this strain a potential candidate for developing a nitrogen-fixing system in rice. Based on genotypic, phenotypic and chemotaxonomic studies, we propose that IR64_4_BI (= MTCC 13051 = JCM 34777) is a new species of Paraburkholderia which has been assigned as Paraburkholderia bengalensis sp.nov.

Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation

The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research. In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed; these methods operate by dividing the input sequence dataset into disjoint sets, constructing trees on each subset, and then combining the subset trees (using auxiliary information) into a tree on the full dataset. DTMs have been used to advantage for multi-locus species tree estimation, enabling highly accurate species trees at reduced computational effort, compared to leading species tree estimation methods. Here, we evaluate the feasibility of using DTMs to improve the scalability of maximum likelihood (ML) gene tree estimation to large numbers of input sequences. Our study shows distinct differences between the three selected ML codes—RAxML-NG, IQ-TREE 2, and FastTree 2—and shows that good DTM pipeline design can provide advantages over these ML codes on large datasets.

Gökkuşağı Alabalıklarından Izole Edilen Chryseobacterium sp. C-204 Suşunun Fenotipik ve Genom Özelliklerinin Belirlenmesi

In recent years, species in the Chryseobacterium genus have emerged as opportunistic fish pathogens that can cause death in fish in many countries. In the last decade, C. aahli, C. oncorhynchi, C. chaponense, and C. piscico-la have been reported to cause systemic infections in fish. In the present study, Chryseobacterium sp. C-204 was iso-lated from 1g weight rainbow trout showing clinical signs such as abnormal swimming, dorsal skin ulceration, darkening in color, and bilateral exophthalmos. The detailed phenotypic characteristics of the C-204 were characterized by API 20NE, and the BIOLOG GEN III system includes 106 phenotypes. Antimicrobial susceptibility of the C-204 was also determined by the broth microdilution method against five antimicrobial agents commonly used in the Aquaculture. Sequence-based identification was done using 16S rRNA genome sequencing. The genome structure of the C-204 was revealed by using next-generation genome sequencing with reading a total of 24195304 bases and assembled in 4012452 base. Genome-based species delineation of C-204 was done 100 different housekeeping gene regions and 50 the closest Chryseobacterium species with Automated Multi-Locus Species Tree (autoMLST, https://automlst.ziemertlab.com). Antimicrobial resistance genes (AMR) and virulence genes in the C-204 genome were iden-tified using the Virulence Factor Database (VFDB) NCBI-reference antimicrobial resistance genes database. The 16S rRNA sequence of C-204 isolate had similarities with the C. aquaticum (99.65%) and C. greenlandense (98.95%) in GenBank. In parallel 19 biochemical tests, C-204 isolate can be differentiated from the closest type strains by nitrate reduction and inability to produce acid from glucose. With regard to antimicrobial susceptibility, the C-204 isolate can grow even at high antimicrobial concentrations determined for Flavobacteriaceae. According to genome-based species delineation, the C-204 isolate was identified as Chryseobacterium aquaticum subsp greenlandense. 13 virulence and eight AMR genes were detected in the genome of the C-204 isolate. Conclusively, the detailed phenotypic characteris-tic includes 106 biochemical test and genome structure of C-204 isolate by whole genome sequencing were deter-mined.

Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world's largest bats (Mammalia: Chiroptera).

Islands provide opportunities for isolation and speciation. Many landmasses in the Indo-Australian Archipelago (IAA) are oceanic islands, and founder-event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group. Australasia, Indo-Australian Archipelago, Madagascar, Pacific Islands. Pteropus (Pteropodidae). To infer the biogeographic history of Pteropus, we sequenced up to 6169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognized Pteropus species and subspecies with 3 Acerodon outgroups using BEAST and subsequently estimated ancestral areas using models implemented in BioGeoBEARS. Species-level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor with Acerodon; founder-event speciation out of Wallacea was a common inference. Pteropus species in Micronesia and the western Indian Ocean were also inferred to result from founder-event speciation. Dispersal between regions of the IAA and the islands found therein fostered diversification of Pteropus throughout the IAA and beyond. Dispersal in Pteropus is far higher than in most other volant taxa studied to date, highlighting the importance of inter-island movement in the biogeographic history of this large clade of large bats.

TreeMerge: a new method for improving the scalability of species tree estimation methods.

MotivationAt RECOMB-CG 2018, we presented NJMerge and showed that it could be used within a divide-and-conquer framework to scale computationally intensive methods for species tree estimation to larger datasets. However, NJMerge has two significant limitations: it can fail to return a tree and, when used within the proposed divide-and-conquer framework, has O(n5) running time for datasets with n species.ResultsHere we present a new method called ‘TreeMerge’ that improves on NJMerge in two ways: it is guaranteed to return a tree and it has dramatically faster running time within the same divide-and-conquer framework—only O(n2) time. We use a simulation study to evaluate TreeMerge in the context of multi-locus species tree estimation with two leading methods, ASTRAL-III and RAxML. We find that the divide-and-conquer framework using TreeMerge has a minor impact on species tree accuracy, dramatically reduces running time, and enables both ASTRAL-III and RAxML to complete on datasets (that they would otherwise fail on), when given 64 GB of memory and 48 h maximum running time. Thus, TreeMerge is a step toward a larger vision of enabling researchers with limited computational resources to perform large-scale species tree estimation, which we call Phylogenomics for All.Availability and implementationTreeMerge is publicly available on Github (http://github.com/ekmolloy/treemerge).Supplementary information Supplementary data are available at Bioinformatics online.

AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential.

Understanding the evolutionary background of a bacterial isolate has applications for a wide range of research. However generating an accurate species phylogeny remains challenging. Reliance on 16S rDNA for species identification currently remains popular. Unfortunately, this widespread method suffers from low resolution at the species level due to high sequence conservation. Currently, there is now a wealth of genomic data that can be used to yield more accurate species designations via modern phylogenetic methods and multiple genetic loci. However, these often require extensive expertise and time. The Automated Multi-Locus Species Tree (autoMLST) was thus developed to provide a rapid ‘one-click’ pipeline to simplify this workflow at: https://automlst.ziemertlab.com. This server utilizes Multi-Locus Sequence Analysis (MLSA) to produce high-resolution species trees; this does not preform multi-locus sequence typing (MLST), a related classification method. The resulting phylogenetic tree also includes helpful annotations, such as species clade designations and secondary metabolite counts to aid natural product prospecting. Distinct from currently available web-interfaces, autoMLST can automate selection of reference genomes and out-group organisms based on one or more query genomes. This enables a wide range of researchers to perform rigorous phylogenetic analyses more rapidly compared to manual MLSA workflows.

Species delimitation and multi-locus species tree solve an old taxonomic problem for European squat lobsters of the genus Munida Leach, 1820

The taxonomy of Munida Leach, 1820 from the north-eastern Atlantic and Mediterranean Sea was studied using a comparative analysis of morphological characters and molecular markers (mitochondrial and nuclear). Generalized Mixed Yule Coalescence and the Poisson tree process models were used to delimit two groups of closely related species associated with uncertain nomenclature and taxonomic status: (1) Munida intermedia A. Milne Edwards & Bouvier, 1899, M. rugosa (Fabricius, 1775), M. sarsi Huus, 1935 and M. tenuimana Sars, 1872 and (2) M. rutllanti Zariquiey-Alvarez, 1952 and M. speciosa von Martens, 1878. We found that M. tenuimana is restricted to northern Atlantic waters (north of approx. 48° N), while Mediterranean and Bay of Biscay specimens previously assigned to this taxon actually belong to a different species, indicating that the name Munida perarmata A. Milne Edwards & Bouvier, 1894 should be resurrected. Furthermore, M. rutllanti is shown to be a junior synonym of M. speciosa, a species that has thus far only been reported along western Africa. In addition, three species are re-described and a key to European Munida is provided. The validity of the morphological characters used to distinguish the different species is discussed. Phylogenetic analyses revealed three independent lineages with unsolved relationships among them, including high genetic distances for some species. These findings indicate highly divergent lineages of the European Munida and several events of colonization along the eastern Atlantic.

Cryptic diversity in Brazilian endemic monkey frogs (Hylidae, Phyllomedusinae, Pithecopus) revealed by multispecies coalescent and integrative approaches

Even though Brazil is the world leader in amphibian diversity, a significant part of its richness remains unknown or hidden under cryptic taxa. Here, we used model-based species delimitation in an integrative taxonomic approach, by gathering molecular and morphometric data to assess cryptic taxa within the monkey frogs Pithecopus rohdei, from the Atlantic Forest, and P. megacephalus, from campos rupestres ecosystem. We sampled one mitochondrial, five nuclear loci, and 18 morphometric variables. Using species-delimitation methods with genetic and morphometric data, we recovered five divergent lineages within P. rohdei and no cryptic lineages were recovered for P. megacephalus. Morphometric data show differentiation only for one of the candidate species revealed by the delimitation approaches, suggesting that individuals from Doce River basin constitute a putative species for formal taxonomic description. The time-calibrated mtDNA tree shows that P. rohdei complex lineages began to diverge in late Miocene. However, dates from the multilocus species tree are more recent, occurring in Pleistocene, and suggesting their persistence in refuges of forest and sky islands within the Atlantic Forest biome. The existence of cryptic taxa within P. rohdei is, therefore, relevant for planning conservation strategies for this species complex in the Atlantic Forest biodiversity hotspot.

A test of the European Pleistocene refugial paradigm, using a Western Palaearctic endemic bird species.

Hewitt's paradigm for effects of Pleistocene glaciations on European populations assumes their isolation in peninsular refugia during glacial maxima, followed by re-colonization of broader Europe during interstadials. This paradigm is well supported by studies of poorly dispersing taxa, but highly dispersive birds have not been included. To test this paradigm, we use the dunnock (Prunella modularis), a Western Palaearctic endemic whose range includes all major European refugia. MtDNA gene tree, multilocus species tree and species delimitation analyses indicate the presence of three distinct lineages: one in the Iberian refugium, one in the Caucasus refugium, and one comprising the Italian and Balkan refugia and broader Europe. Our gene flow analysis suggests isolation of both the Iberian and Caucasus lineages but extensive exchange between Italy, the Balkans and broader Europe. Demographic stability could not be rejected for any refugial population, except the very recent expansion in the Caucasus. By contrast, northern European populations may have experienced two expansion periods. Iberia and Caucasus had much smaller historical populations than other populations. Although our results support the paradigm, in general, they also suggest that in highly dispersive taxa, isolation of neighbouring refugia was incomplete, resulting in large super-refugial populations.

Differentiation of the endemic Greek genus Hymenonema and its relatives of subtribe Scolyminae (Compositae, Cichorieae) based on a multilocus species tree reconstruction

Hymenonema (Compositae, tribe Cichorieae) together with the genera Catananche, Gundelia, and Scolymus forms the subtribe Scolyminae. It is endemic to Greece and consists of two species, Hymenonema laconicum and Hymenonema graecum, which occur in the south Peloponnisos and central Aegean area, respectively. The present contribution aims at a phylogenetic reconstruction of evolutionary relationships among the 12 species of the subtribe, focusing on the temporal and spatial framework for its evolution. The phylogenetic relationships among the members of Scolyminae were inferred from molecular data based on the multi-copy region of the nrDNA internal transcribed spacers ITS1 and ITS2, two intergenic spacers of the cpDNA (trnL-trnF, rpl32-trnL), and one single-copy nuclear region (D10). The gene trees were reconstructed using Bayesian phylogenetic methods. All gene trees support the monophyly of Hymenonema and the sister-group relationship with the genus Scolymus. The further sister-group relationship of this group (Hymenonema–Scolymus) with Catananche is also supported by nrDNA and cpDNA analyses. Finally, a species tree (inferred in a Bayesian coalescent framework) was reconstructed and dates the divergence time between the two Hymenonema species to the Pleistocene (around 1.3 Ma ago). Maximum likelihood-based biogeographical reconstructions suggest a Miocene (pre-Messinian) differentiation of the subtribe on the northern Tethyan platform, followed by Miocene/Pliocene dispersal events to the western Mediterranean and North-African platforms and final, small-scale vicariance events within the genera in the Pleistocene.

SIESTA: enhancing searches for optimal supertrees and species trees

BackgroundMany supertree estimation and multi-locus species tree estimation methods compute trees by combining trees on subsets of the species set based on some NP-hard optimization criterion. A recent approach to computing large trees has been to constrain the search space by defining a set of “allowed bipartitions”, and then use dynamic programming to find provably optimal solutions in polynomial time. Several phylogenomic estimation methods, such as ASTRAL, the MDC algorithm in PhyloNet, FastRFS, and ALE, use this approach.ResultsWe present SIESTA, a method that can be combined with these dynamic programming algorithms to return a data structure that compactly represents all the optimal trees in the search space. As a result, SIESTA provides multiple capabilities, including: (1) counting the number of optimal trees, (2) calculating consensus trees, (3) generating a random optimal tree, and (4) annotating branches in a given optimal tree by the proportion of optimal trees it appears in.ConclusionsSIESTA improves the accuracy of FastRFS and ASTRAL, and is a general technique for enhancing dynamic programming methods for constrained optimization.

Multi-locus reassessment of a striking discord between mtDNA gene trees and taxonomy across two congeneric species complexes

Resolving relationships among members of the yellow and citrine wagtail species complexes is among the greatest challenges in avian systematics due to arguably the most dramatic disagreements between traditional taxonomy and mtDNA phylogeny. Each species complex is divided into three geographically cohesive mtDNA clades. Each clade from one species complex has a sister from the other complex. Furthermore, one cross-complex pair is more distantly related to the remaining two pairs than are several other wagtail species. To test mtDNA gene tree topology, we sequenced the mtDNA ND2 gene and 11 nuclear introns for seven wagtail species. Our mtDNA gene tree reconstruction supported the results of previous studies, thereby confirming the disagreement between mtDNA phylogeny and taxonomy. However, our multi-locus species tree which used mtDNA clades as “taxa” was consistent with traditional taxonomy regardless of whether mtDNA was included in the analysis or not. Our multi-locus data suggest that despite the presence of strongly supported, geographically structured mtDNA variation, the mtDNA gene tree misrepresents the evolutionary history of the yellow and citrine wagtail complexes. This mito-nuclear discord results from mtDNA representing the biogeographic, but not evolutionary history of these recently radiated Palearctic wagtails.

Diversification of deermice (Rodentia: genus Peromyscus) at their north‐western range limit: genetic consequences of refugial and island isolation

AbstractAimWe surveyed the genetic variability of deermice (genus Peromyscus) at the north‐western edge of their range to test for occupancy in multiple, hypothesized ice‐free regions during the late Pleistocene and explore post‐glacial dynamics.LocationNorth‐western North America.MethodsWe used sequences from four independent nuclear and mitochondrial loci from 341 specimens of Peromyscus maniculatus, Peromyscus keeni and Peromyscus sp. (Yukon) to assess species limits, population structure, and demographical change as a result of historical climate change, using a Bayesian approach. Species distribution models were built in MaxEnt to explore the niche overlap amongst genetically distinct species.ResultsDivergence amongst three lineages began before the last interglacial, and each shows signs of post‐glacial expansion. Multilocus species trees strongly support P. keeni and Peromyscus sp. (Yukon) as independent from P. maniculatus. Substantial substructure was observed for P. keeni across the fragmented Alexander Archipelago. Northern lineages or clades (Peromyscus sp. and P. keeni) differed in potential ecological distributions.Main conclusionsAt the extreme north‐western range of deermice in North America, three distinct lineages persist reflecting divergence in at least three ice‐free regions [Beringia, Coastal (near Southeast Alaska) and Southern Continental] throughout the latest Pleistocene glacial cycles. Although spatially proximate in Yukon, no locations were identified where these lineages are in contact. Further, west along the Pacific Coast, P. keeni is widespread across the complex landscape of Southeast Alaska, yet there is limited contemporary gene flow amongst island populations, a finding consistent with the barriers produced by rising sea levels at the end of the Last Glacial Maximum.

Divergence of thermal physiological traits in terrestrial breeding frogs along a tropical elevational gradient.

Critical thermal limits are thought to be correlated with the elevational distribution of species living in tropical montane regions, but with upper limits being relatively invariant compared to lower limits. To test this hypothesis, we examined the variation of thermal physiological traits in a group of terrestrial breeding frogs (Craugastoridae) distributed along a tropical elevational gradient. We measured the critical thermal maximum (CT max; n = 22 species) and critical thermal minimum (CT min; n = 14 species) of frogs captured between the Amazon floodplain (250 m asl) and the high Andes (3,800 m asl). After inferring a multilocus species tree, we conducted a phylogenetically informed test of whether body size, body mass, and elevation contributed to the observed variation in CT max and CT min along the gradient. We also tested whether CT max and CT min exhibit different rates of change given that critical thermal limits (and their plasticity) may have evolved differently in response to different temperature constraints along the gradient. Variation of critical thermal traits was significantly correlated with species’ elevational midpoint, their maximum and minimum elevations, as well as the maximum air temperature and the maximum operative temperature as measured across this gradient. Both thermal limits showed substantial variation, but CT min exhibited relatively faster rates of change than CT max, as observed in other taxa. Nonetheless, our findings call for caution in assuming inflexibility of upper thermal limits and underscore the value of collecting additional empirical data on species’ thermal physiology across elevational gradients.

A permutation approach for inferring species networks from gene trees in polyploid complexes by minimising deep coalescences

SummaryContext and purpose. Due to ubiquity of polyploid species formation in angiosperms, reconstructing the evolutionary history of polyploid complexes is at the forefront of methodological field of activity in molecular phylogenetics and systematic botany. The advent of multilocus species tree reconstruction approaches motivated by next‐generation sequencing methods pave the way to species network inference methods, with which phylogenetics could accommodate to the necessity for reconstructing reticulate relationships among diploids and (allo‐)polyploids in an objective manner, simultaneously taking into account gene tree incongruences caused by incomplete lineage sorting and hybridisation.Methods used. The present contribution describes a relatively simple and fast workflow pipeline for the reconstruction of species networks in polyploid complexes based on multilocus gene trees. It uses a permutation strategy and a parsimony‐based principle in species tree reconstruction (Minimising Deep Coalescences,MDC) for the assignment of homoeologs to parental genomes in allopolyploids, which is a crucial step in species network inference for polyploid complexes. Simulations with varying effective population sizes, different temporal scenarios for diploid or polyploid formations and different types of allopolyploid speciation (sister‐species diploids, non‐sister diploids or polyploidisation under participation of ancestral diploids) are used to assess the reliability of the reconstruction.Main results. Simulations show that the proposed method leads to trustworthy reconstructions if effective populations sizes are not too large and divergences among ancestral taxa are not too shallow. The applicability of our method to a real data set is demonstrated by inferring the reticulate relationships among diploid, tetraploid and hexaploid representatives of the genusLeucanthemopsis(Compositae, Anthemideae) based on gene tree topologies from four nuclear single‐copy genes and two plastidic intergenic spacer regions.Conclusion. The proposedMDC‐based method for species network reconstruction in polyploids is fast and manages to trustworthily reconstruct parentage in polyploidisation events. Concerns with and possible improvements of the described method are discussed.

Taxonomic placement of Onuris hauthalii (Brassicaceae: Eudemeae), based on morphology and multilocus species tree analyses, and the recognition of the new genus Alshehbazia

Fil: Salariato, Diego Leonel. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Botanica Darwinion. Academia Nacional de Ciencias Exactas, Fisicas y Naturales. Instituto de Botanica Darwinion; Argentina

Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys.

BackgroundMultilocus data are becoming increasingly important in determining the phylogeny of closely related species and delimiting species. In species complexes where unequivocal fossil calibrations are not available, rigorous dating of the coalescence-based species trees requires accurate mutation rates of the loci under study but, generally, these rates are unknown. Here, we obtained lineage-specific mutation rates of these loci from a higher-level phylogeny with a reliable fossil record and investigated how different choices of mutation rates and species tree models affected the split time estimates. We implemented this strategy with a genus of water shrews, Neomys, whose taxonomy has been contentious over the last century.ResultsWe sequenced 13 introns and cytochrome b from specimens of the three species currently recognized in this genus including two subspecies of N. anomalus that were originally described as species. A Bayesian multilocus species delimitation method and estimation of gene flow supported that these subspecies are distinct evolutionary lineages that should be treated as distinct species: N. anomalus (sensu stricto), limited to part of the Iberian Peninsula, and N. milleri, with a larger Eurasian range. We then estimated mutation rates from a Bayesian relaxed clock analysis of the mammalian orthologues with several fossil calibrations. Next, using the estimated Neomys-specific rates for each locus in an isolation-with-migration model, the split time for these sister taxa was dated at 0.40 Myr ago (with a 95 % confidence interval of 0.26 – 0.86 Myr), likely coinciding with one of the major glaciations of the Middle Pleistocene. We also showed that the extrapolation of non-specific rates or the use of simpler models would lead to very different split time estimates.ConclusionsWe showed that the estimation of rigorous lineage-specific mutation rates for each locus allows the inference of robust split times in a species tree framework. These times, in turn, afford a better understanding of the timeframe required to achieve isolation and, eventually, speciation in sister lineages. The application of species delimitation methods and an accurate dating strategy to the genus Neomys helped to clarify its controversial taxonomy.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0485-z) contains supplementary material, which is available to authorized users.

Macaronesia is a departure gate of anagenetic speciation in the moss genus Rhynchostegiella

AbstractAimWhy some groups of species radiate, when others appear not to have done so, remains a fundamental question in evolutionary biology. Here, we investigate why island endemism, a common surrogate of speciation rate, reaches its lowest levels among land plants in bryophytes. Using molecular phylogeographical analyses in the moss genus Rhynchostegiella, we contrast the hypotheses (1) that the small size of oceanic islands and moderate genetic isolation in island populations with high dispersal capacities promote lower anagenetic diversification rates than in continental populations, and (2) that island and continental speciation rates do not differ, but island endemics quickly colonize continents.LocationMacaronesia, Europe and Africa.MethodsA time‐calibrated multilocus species tree for 80 populations, representing the nine species of Rhynchostegiella across their entire distribution range, was constructed using beast. Based on this dated tree, ancestral ranges were estimated in BioGeoBears and speciation rates using bamm.ResultsAlthough island‐endemic Rhynchostegiella species evolved anagenetically, speciation rates did not significantly differ between island and continental lineages. Seven episodes of colonization from islands to continental regions were inferred from ancestral‐area estimations, which identified the Canary Islands as the ancestral distribution area of the genus, lending support to our second hypothesis.Main conclusionsOur findings reinforce the view of north‐eastern Atlantic archipelagos as ‘departure gates’ for the colonization of western Europe during the late Pleistocene. They further show that, over longer evolutionary time‐scales, the colonization of continents from island ancestors can lead to speciation and contribute to extant patterns of continental diversity.