Adult and early‐stage characters of Brassolini contain conflicting phylogenetic signal (Lepidoptera,Nymphalidae)

This study examines the contribution of early‐stages and adult characters to the reconstruction of the phylogeny of Brassolini butterflies. Parsimony analyses used both equal weights and implied weights, and a series of analyses were performed. First, we analysed adult and early‐stages partitions independently and in combination for a subset of 27 species; in these cases the matrices were mostly complete. Whereas the adult partition alone produced a topology that was well resolved and congruent with previous studies, the early‐stages partition produced a poorly resolved tree under equal weights. Furthermore, implied weights produced a well‐resolved early‐stages topology that differed significantly from the adult topology. When both partitions were combined for 27 species, implied weights yielded a topology that resembled the adult tree except for the positions of Bia and Penetes, but statistical node support was generally lower. This suggests that stochastic noise increased when early‐stage characters were added to the adult partition, but the combined partitions topology was not statistically different from that based on adult characters alone. Second, given that preserved early stages are not as readily available as adults, we analysed a matrix including 45 species in which early‐stage data were missing for 18 species, and compared the topology to that produced by the adult partition alone. Results were similar to the analyses including fewer species; the combined partitions tree was similar to that from the adult partition except for the position of Bia and Penetes. We compare our findings to other genus‐level phylogenetic studies within Lepidoptera that have also used early‐stages and adult characters.     

Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships,species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)

With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp . ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp , whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets , warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent‐based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.     

Phylogenetic signal in bone histology of amniotes revisited

Legendre, L, Le Roy, N, Martinez‐Maza, C, Montes, L, Laurin, M & Cubo, J. (2012). Phylogenetic signal in bone histology of amniotes revisited. —Zoologica Scripta, 42, 44–53. There is currently a debate about the presence of a phylogenetic signal in bone histological data, but very few rigorous tests have fuelled the discussions on this topic. Here, we performed new analyses using a larger set of seven histological traits and including 25 taxa (nine extinct and 16 extant taxa), using three methods: the phylogenetic eigenvector regression, the tree length distribution and the regressions on distance matrices. Our results clearly show that the phylogenetic signal in our sample of bone histological characters is strong, even after correcting for multiple testing. Most characters exhibit a significant phylogenetic signal according to at least one of our three tests, with the phylogeny often explaining 20–60% of the variation in the histological characters. Thus, we conclude that the phylogenetic comparative method should be systematically used in interspecific analyses of bone histodiversity to avoid problems of non‐independence among observations.     

An improved phylogeny of the Andean tit-tyrants (Aves, Tyrannidae): more characters trump sophisticated analyses

The phylogeny of the flycatcher genus Anairetes was previously inferred using short fragments of mitochondrial DNA and parsimony and distance-based methods. The resulting topology spurred taxonomic revision and influenced understanding of Andean biogeography. More than a decade later, we revisit the phylogeny of Anairetes tit-tyrants using more mtDNA characters, seven unlinked loci (three mitochondrial genes, six nuclear loci), more closely related outgroup taxa, partitioned Bayesian analyses, and two coalescent species-tree approaches (Bayesian estimation of species trees, BEST; Bayesian evolutionary analysis by sampling trees, (*)BEAST). Of these improvements in data and analyses, the fourfold increase in mtDNA characters was both necessary and sufficient to incur a major shift in the topology and near-complete resolution. The species-tree analyses, while theoretically preferable to concatenation or single gene approaches, yielded topologies that were compatible with mtDNA but with weaker statistical resolution at nodes. The previous results that had led to taxonomic and biogeographic reappraisal were refuted, and the current results support the resurrection of the genus Uromyias as the sister clade to Anairetes. The sister relationship between these two genera corresponds to an ecological dichotomy between a depauperate humid cloud forest clade and a diverse dry-tolerant clade that has diversified along the latitudinal axis of the Andes. The species-tree results and the concatenation results each reaffirm the primacy of mtDNA to provide phylogenetic signal for avian phylogenies at the species and subspecies level. This is due in part to the abundance of informative characters in mtDNA, and in part to its lower effective population size that causes it to more faithfully track the species tree.     

PHYLOGENY OF THE HYDRODICTYACEAE (CHLOROPHYCEAE): INFERENCES FROM rDNA DATA1

The hydrodictyacean green algal lineage has been the focus of much research due to the fossil record of at least some members, their ornamented cell walls, and their distinctive reproductive strategies. The phylogeny of the family was, until recently, exclusively morphology based. This investigation examines hydrodictyacean isolates from several culture collections, focusing on sequences from ribosomal data: 18S rDNA, 26S rDNA (partial), and internal transcribed spacer (ITS)‐2 data. Results from phylogenetic analyses of independent and combined data matrices support the Hydrodictyaceae as a monophyletic lineage that includes isolates of Chlorotetraedron, Hydrodictyon, Pediastrum, Sorastrum, and Tetraedron. Phylogenetic analyses of rDNA data indicate that the three‐dimensional coenobium of Hydrodictyon is evolutionarily distinct from the three‐dimensional coenobium of Sorastrum. The more robust aspects of the ITS‐2 data corroborate the 18S+26S rDNA topology and provide a structural autapomorphy for the Hydrodictyaceae and Neochloridaceae, that is, an abridgment of helix IV in the secondary structure. The rDNA data do not support monophyly of Pediastrum but rather suggest the existence of four additional hydrodictyacean genera: Monactinus, Parapediastrum, Pseudopediastrum, and Stauridium.     

The phylogenetic systematics of blue‐tailed skinks (Plestiodon) and the family Scincidae

Blue‐tailed skinks (genus Plestiodon) are a common component of the terrestrial herpetofauna throughout their range in eastern Eurasia and North and Middle America. Plestiodon species are also frequent subjects of ecological and evolutionary research, yet a comprehensive, well‐supported phylogenetic framework does not yet exist for this genus. We construct a comprehensive molecular phylogeny of Plestiodon using Bayesian phylogenetic analyses of a nine‐locus data set comprising 8308 base pairs of DNA, sampled from 38 of the 43 species in the genus. We evaluate potential gene tree/species tree discordance by conducting phylogenetic analyses of the concatenated and individual locus data sets, as well as employing coalescent‐based methods. Specifically, we address the placement of Plestiodon within the evolutionary tree of Scincidae, as well as the phylogenetic relationships between Plestiodon species, and their taxonomy. Given our sampling of major Scincidae lineages, we also re‐evaluate ‘deep’ relationships within the family, with the goal of resolving relationships that have been ambiguous in recent molecular phylogenetic analyses. We infer strong support for several scincid relationships, including a major clade of ‘scincines’ and the inter‐relationships of major Mediterranean and southern African genera. Although we could not estimate the precise phylogenetic affinities of Plestiodon with statistically significant support, we nonetheless infer significant support for its inclusion in a large ‘scincine’ clade exclusive of Acontinae, Lygosominae, Brachymeles, and Ophiomorus. Plestiodon comprises three major geographically cohesive clades. One of these clades is composed of mostly large‐bodied species inhabiting northern Indochina, south‐eastern China (including Taiwan), and the southern Ryukyu Islands of Japan. The second clade comprises species inhabiting central China (including Taiwan) and the entire Japanese archipelago. The third clade exclusively inhabits North and Middle America and the island of Bermuda. A vast majority of interspecific relationships are strongly supported in the concatenated data analysis, but there is nonetheless significant conflict amongst the individual gene trees. Coalescent‐based gene tree/species tree analyses indicate that incongruence amongst the nuclear loci may severely obscure the phylogenetic inter‐relationships of the primarily small‐bodied Plestiodon species that inhabit the central Mexican highlands. These same analyses do support the sister relationship between Plestiodon marginatus Hallowell, 1861 and Plestiodon stimpsonii (Thompson, 1912), and differ with the mitochondrial DNA analysis that supports Plestiodon elegans (Boulenger, 1887) + P. stimpsonii. Finally, because the existing Plestiodon taxonomy is a poor representation of evolutionary relationships, we replace the existing supraspecific taxonomy with one congruent with our phylogenetic results. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 163–189.     

Relationships within Podocarpaceae based on DNA sequence,anatomical, morphological,and biogeographical data

Despite considerable recent progress in understanding intergeneric relationships, a comprehensive analysis of Podocarpaceae at the species level using molecular data, biogeography, anatomy, and morphology has not been previously attempted. Here we present sequence analyses of rbcL, nrITS1 and NEEDLY intron 2 for two‐thirds (183 accessions of 145 taxa) of all Podocarpaceae species representing all genera except Parasitaxus. These analyses include many more species and accessions than previous studies and result in a more resolved phylogeny. The comprehensive anatomical and morphological study ensures that the identification of taxa is correct and also provides clade support. Bayesian and parsimony analyses were used to resolve 20 well‐supported monophyletic groups including 11 groups of the formerly poorly resolved subgenera Podocarpus and Foliolatus. The well‐resolved topology is supported by anatomical and morphological features and is highly congruent with geographical distribution. © The Willi Hennig Society 2011.     

Genome‐wide search for leech antiplatelet proteins in the non‐blood‐feeding leech Helobdella robusta (Rhyncobdellida: Glossiphoniidae) reveals evidence of secreted anticoagulants

The genome of the non‐blood‐feeding glossiphoniid leech Helobdella robusta was screened for leech antiplatelet protein (LAPP), an anticoagulant that specifically inhibits collagen‐stimulated platelet aggregation. Previously identified LAPP sequences from Haementeria officinalis were used as queries against the predicted genes in the genome, employing a variety of BLAST protocols. Matches were reciprocally BLASTed against GenBank databases as a cross‐validation of the predicted annotations of the genes. A total of eight loci, positioned as a tandem array, were recovered with significantly low e‐values; these showed high sequence similarity (32.49% average sequence similarity of shared amino acid positions) to the known anticoagulants. Moreover, six of these possessed a predicted signal‐peptide toward the N‐terminus, indicating their secretion by the leech. All eight loci, together with known LAPP sequences from Ha. officinalis, as well as several sequences from publicly available expressed sequence tag libraries of Ha. depressa and He. robusta, were aligned and subjected to phylogenetic analysis. The resulting tree showed a monophyletic clade consisting of the He. robusta loci, which was sister to a clade comprised of Haementeria‐derived sequences. To corroborate the evolution of the anticoagulants with the evolution of leeches more generally, the topology of the LAPP‐tree was compared to that of a previously published leech phylogeny; these showed compatible topologies with respect to the included genera. These results corroborate recent phylogenetic work, which suggests that this non‐blood‐feeding leech has a hematophagous ancestry.     

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross‐contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.     

Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus)

The use of continuous quantitative characters for phylogenetic analyses has long been contentious in the systematics literature. Recent studies argue for and against their use, but there have been relatively few attempts to evaluate whether these characters provide an accurate estimate of phylogeny, despite the fact that a number of methods have been developed to analyze these types of data for phylogenetic inference. A tree topology will be produced for a given methodology and set of characters, but little can be concluded with regards to the accuracy of phylogenetic signal without an independent evaluation of those characters. We assess the performance of continuous quantitative characters for the mygalomorph spider genus Antrodiaetus, a group that is morphologically homogeneous and one for which few discrete (morphological) characters have been observed. Phylogenetic signal contained in continuous quantitative characters is compared to an independently derived phylogeny inferred on the basis of multiple nuclear and mitochondrial gene loci. Tree topology randomizations, regression techniques, and topological tests all demonstrate that continuous quantitative characters in Antrodiaetus conflict with the phylogenetic signal contained in the gene trees. Our results show that the use of continuous quantitative characters for phylogenetic reconstruction may be inappropriate for reconstructing Antrodiaetus phylogeny and indicate that due caution should be exercised before employing this character type in the absence of other independently derived sources of characters.     

A biogeographic–ecological approach to disentangle reticulate evolution in the Triatoma phyllosoma species group (Heteroptera: Triatominae), vectors of Chagas disease

Introgression and incomplete lineage sorting (ILS) are two of the main sources of gene‐tree incongruence; both can confound the assessment of phylogenetic relationships among closely related species. The Triatoma phyllosoma species group is a clade of partially co‐distributed and cross‐fertile Chagas disease vectors. Despite previous efforts, the phylogeny of this group remains unresolved, largely because of substantial gene‐tree incongruence. Here, we sequentially address introgression and ILS to provide a robust phylogenetic hypothesis for the T. phyllosoma species group. To identify likely instances of introgression prior to molecular scrutiny, we assessed biogeographic data and information on fertility of inter‐specific crosses. We first derived a few explicit hybridization hypotheses by considering the degree of spatial overlap within each species pair. Then, we assessed the plausibility of these hypotheses in the light of each species pair's cross‐fertility. Using this contextual information, we evaluated mito‐nuclear (cyt b, ITS‐2) gene‐tree incongruence and found evidence suggesting introgression within two species pairs. Finally, we modeled ILS using a Bayesian multispecies coalescent approach and either (a) a “complete” dataset with all the specimens in our sample, or (b) a “filtered” dataset without putatively introgressed specimens. The “filtered tree” had higher posterior‐probability support, as well as more plausible topology and divergence times, than the “complete tree.” Detecting and filtering out introgression and modeling ILS allowed us to derive an improved phylogenetic hypothesis for the T. phyllosoma species group. Our results illustrate how biogeographic and ecological‐reproductive contextual information can help clarify the systematics and evolution of recently diverged taxa prone to introgression and ILS.     

Recent origin,active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo‐endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo‐endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)‐based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo‐endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south‐western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long‐distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo‐endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.     

Species tree inference in a recent radiation of orioles (Genus Icterus): multiple markers and methods reveal cytonuclear discordance in the northern oriole group

Recent computational advances provide novel opportunities to infer species trees based on multiple independent loci. Thus, single gene trees no longer need suffice as proxies for species phylogenies. Several methods have been developed to deal with the challenges posed by incomplete and stochastic lineage sorting. In this study, we employed four Bayesian methods to infer the phylogeny of a clade of 11 recently diverged oriole species within the genus Icterus. We obtained well-resolved and mostly congruent phylogenies using a set of seven unlinked nuclear intron loci and sampling multiple individuals per species. Most notably, Bayesian concordance analysis generally agreed well with concatenation; the two methods agreed fully on eight of nine nodes. The coalescent-based method ^∗BEAST further supported six of these eight nodes. The fourth method used, BEST, failed to converge despite exhaustive efforts to optimize the tree search. Overall, the results obtained by new species tree methods and concatenation generally corroborate our findings from previous analyses and data sets. However, we found striking disagreement between mitochondrial and nuclear DNA involving relationships within the northern oriole group. Our results highlight the danger of reliance on mtDNA alone for phylogenetic inference. We demonstrate that in spite of low variability and incomplete lineage sorting, multiple nuclear loci can produce largely congruent phylogenies based on multiple species tree methods, even for very closely-related species.     

Higher‐level phylogenetic affinities of the Neotropical genus Mastigodryas Amaral, 1934 (Serpentes: Colubridae), species‐group definition and description of a new genus for Mastigodryas bifossatus

Most Neotropical colubrid snakes belong to a single, well‐supported lineage. Relationships between the major constituents of this clade remain. Here, we explore the phylogenetic relationships of Mastigodryas and its affinities to other Neotropical colubrid genera by combining DNA and morphological data. Analyses demonstrate that the concatenation of multiple individuals into a single terminal can mask the detection of new taxa. Further, non‐random missing data and/or taxa in some empirical datasets can bias species tree analyses more than concatenation approaches. Our results place Mastigodryas in a strongly supported clade that includes Drymarchon, Rhinobothryum, Drymoluber, Simophis and Leptodrymus. Mastigodryas bifossatus is more closely related to species of Drymoluber and Simophis than to its congeners. Thus, we erect a new genus to accommodate it and recover a monophyletic Mastigodryas. We highlight the importance of the use of morphological characters to diagnose suprageneric clades by showing that some key external and hemipenial characteristics are phylogenetically informative.     

The phylogeny of charadriiform birds (shorebirds and allies) – reassessing the conflict between morphology and molecules

Multiple molecular analyses provide a congruent and well‐supported phylogeny of the charadriiform family‐level taxa, which conflicts with previous hypotheses based on osteological data. In order to revise the latter and to identify new characters of phylogenetic significance, skeletons of most charadriiform family‐level taxa were examined and 49 characters analysed. Tree topology was sensitive to outgroup choice, but the result of the analysis rooted with Columbidae (doves and pigeons) recovered a monophyletic Scolopaci, Charadrii, and nonturnicid Lari. With regard to the inclusion of Alcidae and Glareolidae in the Lari, the results of the present study are also in better concordance with the new molecular phylogenies than previous analyses of morphological data. Furthermore, for the first time an apomorphy of a clade including Thinocoridae, Pedionomidae, Rostratulidae, and Jacanidae was identified. Inclusion of Turnicidae in the Lari could not be supported, but there is no strong morphological evidence for an alternative placement. Pluvianus shares derived osteological features with the Burhinidae, and its position in the molecular analyses likewise cannot be corroborated with morphological data. Based on the topology of the molecular consensus tree, the ancestral state of selected characters is reconstructed. It is finally noted that recent calibrations of molecular analyses, which indicate an origin of extant charadriiform lineages in the Cretaceous, are based on incorrectly identified fossils. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 161 , 916–934.     

Morphological phylogenetic analysis of Ophrys (Orchidaceae): insights from morpho‐anatomical floral traits into the interspecific relationships in an unresolved clade

Reconstructing the phylogeny of the sexually deceptive orchid genus Ophrys is crucial to our understanding of the evolution of its complex floral morphology. Molecular phylogenetic analyses showed that section Pseudophrys forms a well supported clade with Ophrys bombyliflora, O. tenthredinifera and O. speculum, but were unable to elucidate the relationships between these four groups of taxa. Here we conduct a morphological phylogenetic analysis of this unresolved clade of Ophrys based on a data matrix of 45 macro‐ and micromorphological and anatomical floral characters, using maximum parsimony and Bayesian inference. Our cladistic analysis yielded a single most parsimonious tree and a Bayesian 50% majority‐rule consensus tree which differed in their overall topology but agreed that O. tenthredinifera and O. bombyliflora are not sister groups. The phylogenetic placement of O. tenthredinifera was ambiguous since it shares six valid synapomorphies each with the cluster of O. speculum–O. bombyliflora and with section Pseudophrys. In contrast, O. bombyliflora is most likely the sister group to O. speculum, a finding that rejects an earlier morphological phylogenetic hypothesis and favours the existing molecular trees based on nuclear ITS rather than plastid data. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 454–476.     

Phylogeny of Recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets

Zrzavý, J. & ?i?ánková, V. (2004). Phylogeny of Recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets. — Zoologica Scripta, 33, 311–333. Phylogenetic relationships within the Canidae are examined, based on three genes (cytb, COI, COII) and 188 morphological, developmental, behavioural and cytogenetic characters. Both separate and combined phylogenetic analyses were performed. To inspect the phylogenetic ‘behaviour’ of individual taxa, basic phylogenetic analysis was followed by experimental cladistic analyses based on different data‐partition combinations and taxon‐removal analyses. The following phylogeny of the Recent Canidae is preferred: (1) Urocyon is the most basal canid; (2) Vulpes is a monophyletic genus (including Fennecus and Alopex); (3) the doglike canids (DC) form a clade (=Dusicyon + Pseudalopex + Lycalopex + Cerdocyon + Atelocynus + Chrysocyon + Speothos + Lycaon + Cuon + Canis), split into two subclades, South American and Afro‐Holarctic, with uncertain position of the Chrysocyon + Speothos subclade; (4) Canis is paraphyletic due to the position of Lycaon and Cuon. Otocyon and Nyctereutes are the most problematic canid genera, causing an unresolved branching pattern of Otocyon, Vulpes, Nyctereutes and DC clades. Reclassification of the two basal species of ‘Canis’ into separate genera is proposed (Schaeffia for ‘C.’ adustus, Lupulella for ‘C.’ mesomelas). Although the morphological dataset ranked poorly in both separate and simultaneous analyses (measured by number of minimum‐length topologies, relative number of resolved nodes in the strict consensus of all minimum‐length topologies, consistency and retention indices, nodal dataset influence, and number of extra steps required by the data partition to reach the topology of the combined tree), the morphological synapomorphies represent nearly one quarter of all synapomorphies in the combined tree. Among the hidden morphological support of the combined tree the developmental and behavioural characters are conspicuously abundant.     

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

Modern analytical methods for population genetics and phylogenetics are expected to provide more accurate results when data from multiple genome‐wide loci are analysed. We present the results of an initial application of parallel tagged sequencing (PTS) on a next‐generation platform to sequence thousands of barcoded PCR amplicons generated from 95 nuclear loci and 93 individuals sampled across the range of the tiger salamander (Ambystoma tigrinum) species complex. To manage the bioinformatic processing of this large data set (344 330 reads), we developed a pipeline that sorts PTS data by barcode and locus, identifies high‐quality variable nucleotides and yields phased haplotype sequences for each individual at each locus. Our sequencing and bioinformatic strategy resulted in a genome‐wide data set with relatively low levels of missing data and a wide range of nucleotide variation. structure analyses of these data in a genotypic format resulted in strongly supported assignments for the majority of individuals into nine geographically defined genetic clusters. Species tree analyses of the most variable loci using a multi‐species coalescent model resulted in strong support for most branches in the species tree; however, analyses including more than 50 loci produced parameter sampling trends that indicated a lack of convergence on the posterior distribution. Overall, these results demonstrate the potential for amplicon‐based PTS to rapidly generate large‐scale data for population genetic and phylogenetic‐based research.     

Evolutionary history of tree squirrels (Rodentia,Sciurini) based on multilocus phylogeny reconstruction

Pe?nerová, P. & Martínková, N. (2012). Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction. —Zoologica Scripta, 41, 211–219. Tree squirrels of the tribe Sciurini represent a group with unresolved phylogenetic relationships in gene trees. We used partial sequences of mitochondrial genes for 12S rRNA, 16S rRNA, cytochrome b and d‐loop, and nuclear irbp, c‐myc exon 2 and 3 and rag1 genes to reconstruct phylogenetic relationships within the tribe, maximizing the number of analysed species. Bayesian inference analysis of the concatenated sequences revealed common trends that were similar to those retrieved with supertree reconstruction. We confirmed congruence between phylogeny and zoogeography. The first group that diverged from a common ancestor was genus Tamiasciurus, followed by Palaearctic Sciurus and Indomalayan Rheithrosciurus macrotis. Nearctic and Neotropical Sciurus species formed a monophyletic group that included Microsciurus and Syntheosciurus. Neotropical Sciurini were monophyletic with a putative exception of Syntheosciurus brochus that was included in a polychotomy with Nearctic Sciurus in supertree analyses. Our data indicate that Sciurini tree squirrels originated in the northern hemisphere and ancestors of contemporary taxa attained their current distribution through overland colonization from the nearest continent rather than through trans‐Pacific dispersal.     

Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection

Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas.