A molecular phylogeny of the freshwater-fish genus Rasbora (Teleostei: Cyprinidae) in Sri Lanka reveals a remarkable diversification—And a cryptic species

The diversity of the freshwater-fish genus Rasbora (Cyprinidae) on Sri Lanka (five species) is high compared with the four species reported from the peninsula of India, from which the island's cyprinid fauna is derived. The paucity of characters by which species of Rasbora can be phenotypically distinguished renders field identification difficult, adversely affecting the estimation of populations and distributions, with consequences for conservation and management, increasing also the risk of taxonomic inflation. From a sampling of 90 sites across Sri Lanka and based on phylogenetic and haplotype analyses of sequences of cox1 and cytb mitochondrial, and rag1 and irbp nuclear markers, we review the species diversity and phylogeography of Rasbora on the island. Molecular analyses recover, in addition to the five species previously reported, a new (cryptic) species: Rasbora adisi sp. nov. Uncorrected pairwise cox1 genetic distances between species range from 2.0 to 12.3 percent. The Sri Lankan diversification derives from a common ancestor which arrived from India during a sea-level low-stand in the mid-Miocene (15.1 Ma [95% HPD: 11.5–19.8 Ma]), when the present-day island was subaerially connected to the Indian subcontinent by a broad isthmus. This gave rise to a clade comprising five species—R. adisi sp. nov.,Rasbora armitagei, Rasbora microcephalus, Rasbora naggsi and Rasbora wilpita—with a crown age of 9.9 Ma (95% HPD: 7.1–13.3 Ma) and to a clade comprising Indian and Sri Lankan populations of Rasbora dandia, which themselves are reciprocally monophyletic. Morphological analysis of 334 specimens discriminates between most species which, however, are most reliably diagnosed by chromatic characters. The four endemic species exhibit a pattern of inter-basin dispersal via headwater capture, followed by vicariance, explaining the high diversity of the genus on the island.     

Cryptic speciation in the narrow‐headed vole Lasiopodomys (Stenocranius) gregalis (Rodentia: Cricetidae)

Recent study on Lasiopodomys (Stenocranius) gregalis has revealed four clear mitochondrial lineages with differences exceeding the species level. The most divergent is the clade from south‐eastern Transbaikalia. Multilocus (six nuclear genes), morphological (dental characters of m1 and M3) and behavioural (breeding experiments) analyses were conducted to test the hypothesis that L. gregalis is a complex of two cryptic species. All of the applied methods distinguish the independent status of voles from south‐eastern Transbaikalia. This clade occupies a portion of the distribution range of the currently valid subspecies L. g. raddei including its terra typica. According to the results of cyt b analysis, the lectotype of L. g. raddei belongs to the Transbaikal clade. We re‐establish the species status for the taxon Lasiopodomys raddei including populations from south‐eastern Transbaikalia, as a cryptic species of the narrow‐headed vole complex.     

Integrative taxonomy of the Rhinolophus macrotis complex (Chiroptera,Rhinolophidae) in Vietnam and nearby regions

The taxonomic status of Rhinolophus macrotis sensu lato (s.l.) in Vietnam and adjacent territories remains problematic. To address this issue, we performed an integrated study of morphological, acoustic, and genetic characters of R. macrotis s.l. specimens and compared these with sympatric species within the philippinensis group (R. marshalli, R. paradoxolophus, and R. rex). Our results reveal that in addition to a cryptic species of R. macrotis previously found in Jiangxi and Jingmen, China, R. macrotis s.l. in continental Asia includes three further species, namely R. cf. siamensis, R. cf. macrotis, and R. cf. macrotis “Phia Oac.” These four taxa are distinguished from genuine R. macrotis in Nepal and R. siamensis in Thailand by their morphological and/or genetic features. Further taxonomic evaluation of the subspecies of R. macrotis s.l. is needed to determine their affinities with recently recognized cryptic species and to possibly describe new taxa. Our results also show that interspecific divergences in mitochondrial DNA sequences (Cytb and COI genes) among taxa within the philippinensis group (particularly between R. cf. siamensis/R. cf. macrotis and R. rex/R. paradoxolophus) are significantly lower than those of other morphological groups in the genus. These phylogenetic patterns might be explained by recent allopatric speciation or ancient introgression events among ancestors of the taxa during the Pleistocene. However, further investigations including genetic analyses of nuclear genes are needed to test the latter hypothesis.     

Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, <Emphasis Type="Italic">Buteo jamaicensis harlani</Emphasis>

Background  

Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations.     

Phylogeny of Impatiens (Balsaminaceae): integrating molecular and morphological evidence into a new classification

Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty‐six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB‐rbcL and trnL‐F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum‐parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three‐colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well‐supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.     

Phylogeny of Rhigonematomorpha based on the complete mitochondrial genome of Rhigonema thysanophora (Nematoda: Chromadorea)

We determined the complete mitochondrial genome sequence of Rhigonema thysanophora, the first representative of Rhigonematomorpha, and used this sequence along with 57 other nematode species for phylogenetic analyses. The R. thysanophora mtDNA is 15 015 bp and identical to all other chromadorean nematode mtDNAs published to date in that it contains 36 genes (lacking atp8) encoded in the same direction. Phylogenetic analyses of nucleotide and amino acid sequence data for the 12 protein‐coding genes recovered Rhigonematomorpha as the sister group to the heterakoid species, Ascaridia columbae (Ascaridomorpha). The organization of R. thysanophora mtDNA resembles the most common pattern for the Rhabditomorpha+Ascaridomorpha+Diplogasteromorpha clade in gene order, but with some substantial gene rearrangements. This similarity in gene order is in agreement with the sequence‐based analyses that indicate a close relationship between Rhigonematomorpha and Rhabditomorpha+Ascaridomorpha+Diplogasteromorpha. These results are consistent with certain analyses of nuclear SSU rDNA for R. thysanophora and some earlier classification systems that asserted phylogenetic affinity between Rhigonematomorpha and Ascaridomorpha, but inconsistent with morphology‐based phylogenetic hypotheses that suggested a close (taxonomic) relationship between rhigonematomorphs and oxyuridomorphs (pinworms). These observations must be tempered by noting that few rhigonematomorph species have been sequenced and included in phylogenetic analyses, and preliminary studies based on SSU rDNA suggest the group is not monophyletic. Additional mitochondrial genome sequences of rhigonematids are needed to characterize their phylogenetic relationships within Chromadorea, and to increase understanding of mitochondrial genome evolution.     

Cryptic diversity in disjunct populations of Middle American Montane Pitvipers: a systematic reassessment of Cerrophidion godmani

Jadin, R.C., Townsend, J.H., Castoe, T.A. & Campbell, J.A. (2012). Cryptic diversity in disjunct populations of Middle American Montane Pitvipers: a systematic reassessment of Cerrophidion godmani. —Zoologica Scripta, 41, 455–470. The discovery and taxonomic recognition of cryptic species has become increasingly frequent with the application of molecular phylogenetic analyses, particularly for species with broad geographic distributions. In this study we focus on the venomous pitviper species Cerrophidion godmani that is widely distributed throughout the highlands of Central America. We provide evidence based on both molecular phylogenetic analyses and morphological data that C. godmani represents three deeply divergent lineages and is possibly non‐monophyletic. These three lineages are relatively conserved in their morphology and tend to be highly variable among individuals, but we do find sufficient morphological characters to diagnose them as evolutionarily distinct. We apply these data, together with known geographic distributions of populations, to infer boundaries of these three divergent evolutionary lineages. Based on the body of evidence, we formally name and describe two new species of Cerrophidion and redescribe C. godmani sensu stricto.     

Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae)

Hypotheses on the taxonomic status of two Bolivian Pristimantis with taxonomic problems are assessed by an integrative taxonomic approach that integrates three independent lines of evidence: external morphology, prezygotic reproductive barriers (advertisement calls) and reciprocal monophyly (phylogenetic analyses of partial 16S mtDNA sequences). Central Andean Bolivian populations previously assigned to either P. peruvianus or P. dundeei, and lowland Amazonian populations from southern Peru and northern Bolivia previously considered P. peruvianus do not correspond to these species. Indeed, multivariate analyses of qualitative and quantitative morphological and bioacoustic characters, and phylogenetic analyses support the hypothesis that they represent different, previously unknown, cryptic lineages. They are herein described as new species. The former is a sibling species of P. fenestratus that inhabits the Amazonian and semideciduous forests of the Andean foothills in central Bolivia. The latter is sibling to the Andean species P. danae and is parapatric to it in the Amazonian lowland forests and adjacent foothills of northern Bolivia, southern Peru and adjacent Brazil. Most species of Neotropical frogs, and especially Pristimantis, have been described by using external qualitative morphological characters only. An extended integrative taxonomic approach, as exemplified herein, may lead to the discovery of many other cryptic and sibling lineages that would increase the species numbers of tropical areas. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 97–122.     

Phylogeography of the pallid kangaroo mouse,Microdipodops pallidus: a sand‐obligate endemic of the Great Basin,western North America

Aim Kangaroo mice, genus Microdipodops Merriam, are endemic to the Great Basin and include two species: M. pallidus Merriam and M. megacephalus Merriam. The pallid kangaroo mouse, M. pallidus, is a sand‐obligate desert rodent. Our principal intent is to identify its current geographical distribution and to formulate a phylogeographical hypothesis for this taxon. In addition, we test for orientation patterns in haplotype sharing for evidence of past episodes of movement and gene flow. Location The Great Basin Desert region of western North America, especially the sandy habitats of the Lahontan Trough and those in south‐central Nevada. Methods Mitochondrial DNA sequence data from portions of three genes (16S ribosomal RNA, cytochrome b, and transfer RNA for glutamic acid) were obtained from 98 individuals of M. pallidus representing 27 general localities sampled throughout its geographical range. Molecular sequence data were analysed using neighbour‐joining, maximum‐parsimony, maximum‐likelihood and Bayesian methods of phylogenetic inference. Directional analysis of phylogeographical patterns, a novel method, was used to examine angular measurements of haplotype sharing between pairs of localities to detect and quantify historical events pertaining to movement patterns and gene flow. Results Collecting activities showed that M. pallidus is a rather rare rodent (mean trapping success was 2.88%), and its distribution has changed little from that determined three‐quarters of a century ago. Two principal phylogroups, distributed as eastern and western moieties, are evident from the phylogenetic analyses (mean sequence divergence for cytochrome b is c. 8%). The western clade shows little phylogenetic structure and seems to represent a large polytomy. In the eastern clade, however, three subgroups are recognized. Nine of the 42 unique composite haplotypes are present at two or more localities and are used for the orientation analyses. Axial data from haplotype sharing between pairwise localities show significant, non‐random angular patterns: a north‐west to south‐east orientation in the western clade, and a north‐east to south‐west directional pattern in the eastern clade. Main conclusions The geographical range of M. pallidus seems to be remarkably stable in historical times and does not show a northward (or elevationally upward) movement trend, as has been reported for some other kinds of organism in response to global climate change. The eastern and western clades are likely to represent morphologically cryptic species. Estimated times of divergence of the principal clades of M. pallidus (4.38 Ma) and between M. pallidus and M. megacephalus (8.1 Ma; data from a related study) indicate that kangaroo mice diverged much earlier than thought previously. The phylogeographical patterns described here may serve as a model for other sand‐obligate members of the Great Basin Desert biota.     

How many marmoset (Primates: Cebidae: Callitrichinae) genera are there? A phylogenetic analysis based on multiple morphological systems

The marmosets, tribe Callitrichini, are the most speciose clade in the subfamily Callitrichinae, containing 21 species. However, there is no consensus among molecular and morphological systematists as to how many genera should be recognized for the group. To test the morphological support for the alternative generic classifications, this study presents a comprehensive phylogenetic analysis. It is the first such analysis to include all 21 species and employ continuous and discrete osteological, pelage and tegument, karyological and vocal characters. This dataset was combined with nucleotide sequences from two mitochondrial and four nuclear regions. Separate analyses showed that, among morphological datasets, osteological characters were best at solving relationships at more inclusive levels, whilst pelage characters were most informative at the interspecific level. This suggests the presence of different transformation rates for the two character sets. When a single most parsimonious tree was obtained using the 83‐character matrix, three main clades were identified, supporting the division of the marmosets into three genera: Callithrix, Cebuella and Mico. The total evidence analysis that included an additional 3481 molecular characters corroborated most of the morphology‐based clades and also supported a three‐genus classification of the marmosets. This is the first morphological study to support an Amazonian marmoset clade (Cebuella + Mico), which is also strongly supported in exclusively molecular phylogenies, and to synonimize Callibella under Mico.     

Diversity in the genus Rhabdias (Nematoda,Rhabdiasidae): Evidence for cryptic speciation

Lungworms from the genus Rhabdias are common parasites of amphibians and reptiles distributed worldwide. To assess the diversity of Rhabdias spp., we performed molecular analyses of 35 specimens sampled in different regions of Brazil. Molecular analyses were based on the internal transcribed spacer (ITS), large subunit (28S) ribosomal and the cytochrome oxidase I (COI) mitochondrial genes. DNA sequence divergence was compared among ribosomal and mitochondrial genes, analyses using the general mixed Yule‐coalescent (GMYC) method based on the COI gene were used to identify possible cryptic diversity, and phylogenetic analyses using concatenated ITS and 28S ribosomal genes were used to test the monophyly of Rhabdiasidae. We revealed five morphospecies: R. cf. stenocephala, R. breviensis, R. pseudosphaerocephala and two new species, Rhabdias sp.4 and Rhabdias sp.5. DNA sequence levels of divergence among genes ITS, 28S and COI were compared, and the efficiency of the molecular markers to identify species (ITS and COI) and lineages (COI) was tested. GMYC was assigned to 17 well‐supported clades (i.e., 17 species), and cryptic diversity was detected in the Neotropical region as evidenced by the multiple lineages in R. breviensis and R. pseudosphaerocephala. In addition, our results suggest evidence for host–parasite cophylogeny in the R. pseudosphaerocephala complex and dispersal events among their populations. Phylogenetic analyses supported the monophyly of Rhabdiasidae and improved the resolution of main clades. Rhabdias breviensis is closely related to Rhabdias cf. africanus, Rhabdias cf. stenocephala, R. pseudosphaerocephala, Rhabdias sp.4 and Rhabdias sp.5 grouping together in a main clade with Neotropical‐related species. The large geographical distribution appeared to be a phylogenetic pattern among the species of Rhabdias from the neotropics.     

Unmasking cryptic species: morphometric and phylogenetic analyses of the Ibero‐North African Linaria incarnata complex

Linaria incarnata has been treated as a widely distributed Ibero‐North African species in the latest taxonomic reviews. Morphological and phylogenetic disparity between populations of this species has been previously reported. Here we present new morphological and phylogenetic evidence for the disintegration of L. incarnata into three distinct species: L. incarnata from the western Iberian Peninsula; L . mamorensis sp. nov. from north‐western Morocco; and L. onubensis from south‐western Spain. The relatively poor morphological differentiation between these taxa (which can be regarded as cryptic species) and their distinct phylogenetic positions indicate that characters of the L. incarnata morphotype have been acquired multiple times in the evolution of Linaria section Versicolores. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 00, 000–000.     

The striking polyphyly of Suiriri: Convergent evolution and social mimicry in two cryptic Neotropical birds

Two species of Suiriri (Aves: Tyrannidae) inhabit semi‐open habitats in South America: the polytypic Suiriri Flycatcher (S. suiriri) and the monotypic Chapada Flycatcher (S. affinis). The phylogenetic relationship between these congeneric species has never been investigated in detail. Here we used molecular tools—three nuclear introns and two mitochondrial genes—to investigate the systematic position of the Chapada Flycatcher, comparing the results found with morphological and behavioral data. We found that the polytypic Suiriri Flycatcher to be monophyletic and that it is included in a clade of Elaeniini flycatchers including Phyllomyias, Phaeomyias, and Capsiempis among other genera. The Chapada Flycatcher, on the other hand, is a member of the Fluvicolini, sister to Sublegatus, and should be allocated on its own monospecific genus, which we herein describe. We suggest that social mimicry is responsible for the remarkable convergence in size, shape, plumage coloration, and behavior in the adults of the Suiriri Flycatcher and the Chapada Flycatcher.     

Phylogenetic relationships within a patagonian clade of reptiles (Liolaemidae: Phymaturus) based on DNA sequences and morphology

Phymaturus is a clade of lizards that occurs at moderate to high elevations in western Argentina and the adjacent central region of Chile, as well as in various volcanic plateaus of the Patagonian region of Argentina. This genus had previously been divided into two groups: the patagonicus and the palluma groups. In this study, we analyzed relationships within the patagonicus group. The data set was built for 23 species plus nine other terminal taxa of undetermined taxonomic status. In total, 10,631 bp (ND4, Cytb, 12S, COI, five protein coding nuclear genes and seven anonymous nuclear loci) and 254 morphological characters were analyzed in a combined data set for 35 ingroup taxa and nine outgroups. We also ran separate DNA sequence and morphological data sets. We identified four main clades, and revealed congruencies and incongruences with previous studies. The indistinctus clade is recovered as the most basal within the patagonicus group in the strict parsimony analysis, while the somuncurensis clade is the most basal under Bayesian inference. The previously recovered calcogaster clade resulted paraphyletic in both analyses and part of their species are included in a redefined somuncurensis clade. We found low support at basal nodes provoked in part by contradictory evidence shown by rogue taxa. We show the phylogenetic information given by each partition/marker and how they contribute to relationships found in the total evidence analysis. We discuss the phylogenetic position of Phymaturus manuelae, Phymaturus tenebrosus, and Phymaturus patagonicus.     

Phylogenetic relationships of toads of the Rhinella granulosa group (Anura: Bufonidae): a molecular perspective with comments on hybridization and introgression

The Rhinella granulosa group consists of 13 species of toads distributed throughout open areas of South America and Panama. In this paper we perform a phylogenetic analysis considering all but one species of the group, employing five nuclear and four mitochondrial genes, for up to 7910 bp per specimen. Separate phylogenetic analyses under direct optimization (DO) of nuclear and mitochondrial sequences recovered the R. granulosa group as monophyletic and revealed topological incongruence that can be explained mainly by multiple events of hybridization and introgression, both mitochondrial and nuclear. The DO combined analysis, after the exclusion of putatively introgressed or heterozygous genomes, resulted in a phylogenetic hypothesis for the R. granulosa group in which most of the species are recovered as monophyletic, but with interspecific relationships poorly supported. The optimization of morphological (adult and larval), chromosomal, and behavioural characters resulted in 12 putative phenotypic synapomorphies for this species group and some other synapomorphies for internal clades. Our results indicate the need for additional population genetic studies on R. dorbignyi and R. fernandezae to corroborate the taxonomic status of both taxa. Finally, we discuss biological and genetic characteristics of Bufonidae, as possible explanations for the common occurrence of hybridization and introgression observed in some lineages of this family.     

Prevalence,geographic distribution and phylogenetic relationships among cryptic species of Plasmopara viticola in grape‐producing regions of Georgia and Florida,USA

Previous phylogenetic studies of the grape downy mildew pathogen, Plasmopara viticola, revealed five cryptic species in eastern North America that differed in their host range and geographic distribution. Preliminary comparative studies also documented differences in temperature responses during infection between certain cryptic species, indicating the biological relevance of knowing which cryptic species of the pathogen are present in a given region. However, limited information is available regarding the presence, prevalence and dynamics of cryptic species of P. viticola in the southeastern United States. Here, 301 P. viticola isolates obtained from cultivated grape species in five distinct grape‐growing regions of Georgia and Florida were subjected to cleaved amplified polymorphic sequence analysis and multilocus sequencing (internal transcribed spacer region of the rDNA, actin and β‐tubulin) to identify cryptic species and infer phylogenetic relationships. Three cryptic species, P. viticola clade aestivalis (Pva), clade vinifera (Pvv) and clade vulpina (Pvu), were identified in Georgia, whereas two, Pva and Pvv, were found in Florida; all three cryptic species are reported here for the first time in Georgia, whereas Pva is reported for the first time in Florida. Pva was the most prevalent cryptic species (72.1% of isolates) and was distributed widely from the North Georgia Mountains to Mid‐Florida, whereas Pvv (27.2%) and Pvu (0.7%) were found only in the Coastal Plain region of the two states. Interestingly, Pvu was obtained from French American hybrid Blanc du Bois and could be subcultured on Vitis vinifera Chardonnay, suggesting a broader host range than only the wild species Vitis vulpina reported previously.     

Taxonomy of cryptic species in the Cyornis rubeculoides complex in the Indian subcontinent

Taxa classified as subspecies may in fact be cryptic species. We assessed the taxonomic status of the Blue-throated Flycatcher Cyornis rubeculoides complex in India, which consists of several forms with similar plumages and song. We used mitochondrial and nuclear DNA, plumage traits, and detailed song analysis to ascertain the taxonomic status of the different forms. The molecular data identified three primary clades: (1) in the west Himalayan foothills, (2) at higher elevations in the northeast hill states of Meghalaya, Nagaland and Mizoram, and (3) at lower elevations in the northeastern hills of Meghalaya and the east Himalayas of Arunachal Pradesh. The western clade represents nominate C. rubeculoides rubeculoides. The high-elevation eastern clade was considered to be C. rubeculoides rogersi, because it included a sample from this subspecies from near the type locality in southwest Myanmar. These two sister clades had an estimated divergence time of 1.5 million years (my). The low-elevation east clade has previously been assigned to C. rubeculoides, but we showed it is closely related to the Hainan Blue Flycatcher Cyornis hainanus, formerly thought to breed only further east, with an estimated divergence time of only ~0.8 my. This clade may represent a subspecies of C. hainanus or, given reports of widespread sympatry with C. hainanus in Thailand, a distinct species, Cyornis dialilaemus. However, more research is advocated, including molecular data, from the area of overlap. Songs were remarkably similar across all taxa. In playback experiments, C. r. rubeculoides in the west responded to all taxa. This is in agreement with recent work demonstrating that song differences and responses to songs are not always a good indicator of the progress of reproductive isolation.     

Classification of crucigenoid algae: phylogenetic position of the reinstated genus Lemmermannia,Tetrastrum spp. Crucigenia tetrapedia,and C. lauterbornii (Trebouxiophyceae,Chlorophyta)1

The subfamily Crucigenioideae was traditionally classified within the well‐characterized family Scenedesmaceae (Chlorophyceae). Several morpho‐logical revisions and questionable taxonomic changes hampered the correct classification of crucigenoid species resulting in a high number of synonymous genera. We used a molecular approach to determine the phylogenetic position of several Tetrastrum and Crucigenia species. The molecular results were correlated with morphological and ontogenetic characters. Phylogenetic analyses of the SSU rDNA gene resolved the position of Tetrastrum heteracanthum and T. staurogeniaeforme as a new lineage within the Oocystis clade of the Trebouxiophyceae. Crucigenia tetrapedia, T. triangulare, T. punctatum, and T. komarekii were shown to be closely related to Botryococcus (Trebouxiophyceae) and were transferred to Lemmer‐mannia. Crucigenia lauterbornii was not closely related to the other Crucigenia strains, but was recovered within the Chlorella clade of the Trebouxiophyceae.