Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae)

Ainscough, B.J., Breinholt, J.W., Robison, H.W. & Crandall, K.A. (2013). Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae). —Zoologica Scripta, 42, 306–316. The crayfish genus Fallicambarus contains 19 species of primary burrowing freshwater crayfish divided into two distinct subgenera. We test current hypotheses of the phylogenetic relationships among species within the genus as well as the monophyly of the genus. Our study samples all 19 species for five gene regions (both nuclear and mitochondrial) to estimate a robust phylogenetic hypothesis for the genus. We show that the genus is not a monophyletic group. The subgenus Creaserinus does fall out as a monophyletic group, but distinct from the subgenus Fallicambarus. The subgenus Fallicambarus appears to be monophyletic with the exception of the species Procambarus (Tenuicambarus) tenuis, which falls in the midst of this subgenus suggesting that it might be better classified as a Fallicambarus species. We also show that the species Fallicambarus fodiens is a species complex with distinct evolutionary lineages that are regionalized to different geographic areas.     

Molecular phylogeny of the marine littoral genus Cafius (Coleoptera: Staphylinidae: Staphylininae) and implications for classification

Jeon, M.‐J., Song, J.‐H. & Ahn, K.‐J. (2012). Molecular phylogeny of the marine littoral genus Cafius (Coleoptera: Staphylinidae: Staphylininae) and implications for classification. —Zoologica Scripta, 41, 150–159. A phylogenetic analysis of the marine littoral genus Cafius Stephens is presented based on molecular characters. The data set comprised partial mitochondrial COI (910 bp), COII (369 bp), 12S rDNA (351–354 bp), 16S rDNA (505–509 bp) and nearly complete sequences of 18S rDNA (1814–1830 bp) for 37 species. Twenty‐seven Cafius species, representing five of six subgenera, two Remus Holme species, three Phucobius Sharp species, monotypic Thinocafius Steel and four outgroups were included. The sequences were analysed simultaneously by parsimony analysis in Tree Analysis Using New Technology (TNT) with traditional manual alignment, direct optimization (DO) in the program POY4 under a variety of gap costs and partitioned Bayesian analysis for the combined data. The genus Cafius and nearly all of its subgenera were not supported as being monophyletic. Instead, all analyses (parsimony trees, DO tree under equal weighting and Bayesian tree) showed monophyly of Cafius + Phucobius + Remus + Thinocafius (clade Z) and all seven nested clades (A–G). However, the phylogenetic relationships among clades A–G differed among the analyses. The genus Phucobius was recovered as a monophyletic group within Cafius. The genus Remus was not monophyletic but formed a clade with C. rufescens Sharp and C. rufifrons Bierig within Cafius. The genus Thinocafius formed a clade with C. caviceps Broun, C. litoreus (Broun) and C. quadriimpressus (White) within Cafius. We propose new concepts for the genus Cafius and its related genera, and the seven nested clades.     

Molecular phylogeny of the subgenus Holothuria (Selenkothuria) Deichmann, 1958 (Holothuroidea: Aspidochirotida)

The subgenus Selenkothuria comprises 12 species of tropical shallow water sea cucumbers that share morphological features, such as rods in the body wall and tube feet, modified tentacles for suspension feeding, and cryptic colours. The taxonomic status of this taxon has been controversial, but currently it is accepted as a subgenus of the genus Holothuria. Phylogenetic analyses of mitochondrial genes [cytochrome c oxidase subunit 1 (COI), 16S RNA] of ten species of Selenkothuria and related subgenera showed the polyphyly of this subgenus; monophyly was rejected by a likelihood ratio test. A geographical split divides the species of this subgenus into three different groups: one Indo‐West‐Pacific (IWP) group and two American groups. The IWP group is more closely related to Holothuria (Semperothuria) cinerascens and to other subgenera such as Roweothuria, Holothuria, and Vaneyothuria, whereas the two American groups are more closely related to each other and to some species of the subgenus Halodeima. These results suggest multiple parallel originations and diversification of ossicle morphology within the subgenus Selenkothuria. The current scheme of subgenera for the genus Holothuria is not supported, suggesting the need for a new classification. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 109–120.     

Reconsideration of anopheline mosquito phylogeny (Diptera: Culicidae: Anophelinae) based on morphological data

The phylogeny of anopheline mosquitoes (Culicidae: Anophelinae) is re‐examined using morphological data derived from adults, fourth‐instar larvae and pupae. Based on the data set of Sallum et al. (2000), we add some previously missing data and simplify and recode characters to eliminate ambiguities and more accurately reflect homologies, with special emphasis on characters of the male genitalia that provide the main criteria for the subgeneric classification of genus Anopheles. The principal aim of the study is to assess objectively the phylogenetic relationships and classification of two taxa not included by Sallum et al. (2000): Anopheles corethroides, a representative of the Australasian Stigmaticus Group, and An. kyondawensis, an unusual Oriental species whose adult and pupal stages were only recently discovered. The revised data set consists of 167 characters for 66 species representing the three traditionally recognised genera of Anophelinae, the six traditionally accepted subgenera of genus Anopheles and all informal series and most species groups of subgenera Anopheles, Cellia and Nyssorhynchus. The data are analysed using equal weighting (EW) and implied weighting (IW). Analysis under EW generates a strict consensus tree with principal lineages consistent with those reported by Sallum et al. (2000). Analysis under IW supports the monophyly of Anophelinae, the basal position of Chagasia, the monophyly of subgenera Cellia, Kerteszia and Nyssorhynchus, and the sister relationship of Kerteszia + Nyssorhynchus, but otherwise yields relationships that differ significantly in one respect or another from those obtained in all previous analyses of both morphological and molecular data. Subgenus Anopheles is arrayed as a polyphyletic lineage basal to a monophyletic clade comprising the Neotropical Kerteszia + Nyssorhynchus and the Old World Cellia in a sister‐group relationship. Bironella, Lophopodomyia and Stethomyia are firmly nested within subgenus Anopheles, which would nevertheless still be paraphyletic if these taxa were subsumed within it. Anopheles kyondawensis is well supported as the sister group of Bironella + all other Anopheles. Bironella, Stethomyia, An. corethroides and several other Anopheles clades are each strongly supported in a pectinate series of relationships, terminating in the clade comprising subgenera Cellia, Kerteszia and Nyssorhynchus. These relationships and other aspects of the phylogeny are discussed in relation to the formal and informal classification of genus Anopheles.     

A review of cross‐backed grasshoppers of the genus Dociostaurus Fieber (Orthoptera: Acrididae) from the western Mediterranean: insights from phylogenetic analyses and DNA‐based species delimitation

Phylogenetic analyses and species delimitation methods are powerful tools for understanding patterns of species diversity. Given the current biodiversity crisis, such approaches are invaluable for urgent assessment and delimitation of truthful species, particularly of endangered and morphologically cryptic taxa from vulnerable areas submitted to strong climate change and progressive human intervention such as the M editerranean region. In this study, we applied two DNA ‐based species delimitation methods and performed a B ayesian phylogenetic reconstruction using three mitochondrial gene fragments (12S , 16S and COI) to solve several taxonomic uncertainties among species of cross‐backed grasshoppers (genus Dociostaurus F ieber) from the western M editerranean. P hylogenetic analyses demonstrate the polyphyletic character of subgenera Dociostaurus , Kazakia B ey‐B ienko and Stauronotulus T arbinsky and, thus, the necessity of revising the currently accepted taxonomic subgenera within the genus Dociostaurus . We propose the split of closely related taxa with allopatric distributions such as D. (S.) kraussi and D. (S.) crassiusculus , considering the later a distinct species limited to the I berian P eninsula and excluding the name crassiusculus from other forms of D. (S.) kraussi from E ast E urope and A sia. Estimates of divergence times indicate that diversification of Dociostaurus probably happened during the M iocene–P liocene (3–7 Ma), and the split of the studied pairs of sister taxa took place during the middle and late P leistocene (1–2 Ma). This study highlights the need for more molecular studies on the genus and their different species for a better understanding of their evolution, genetic variation and population dynamics in order to prioritize strategies for their adequate conservation and management.     

Taxonomy of the long‐tailed mouse Oligoryzomys destructor (Sigmodontinae: Oryzomyini) with the designation of neotypes for Hesperomys destructor Tschudi, 1844 and Hesperomys melanostoma Tschudi, 1844

The genus Oligoryzomys, distributed from southern South America to southern North America, is the most diverse of the tribe Oryzomyini of sigmodontine rodents. Even when 22 species are currently recognized, species boundaries are unclear for several forms. The species Oligoryzomys destructor is one of the least studied species of the genus and is the one with the largest distribution along the Andes (from southern Colombia to northern Bolivia). The species was described without the selection of a holotype and indication of its type locality. In addition, several taxa are regarded as synonyms of O. destructor. These facts are relevant because previous analysis of DNA sequences has shown that O. destructor represents a species complex. Herein, in addition to test the phylogenetic position of O. destructor within the genus Oligoryzomys, we assess patterns of morphological and molecular variation of O. destructor and its associated nominal forms aimed to assess the boundaries of the species. As part of the study, we selected neotypes for Hesperomys destructor and H. melanostoma. At the light of our results, we recognized O. destructor as a species with two subspecies, O. d. destructor and O. d. spodiurus. Also, we discuss the role of Andean rivers, and their different permeability, as allopatric barriers molding the structure of O. destructor.     

Phylogeny of leafcutter ants in the genus Atta Fabricius (Formicidae: Attini) based on mitochondrial and nuclear DNA sequences

Leafcutting ants of the genus Atta are the most conspicuous members of the tribe Attini, the fungus-growing ants. Atta species have long attracted the attention of naturalists, and have since become a common model system for the study of complex insect societies as well as for the study of coevolutionary dynamics due to their numerous interactions with fungi and other microbes. Nevertheless, systematics and taxonomy of the 15 species in the genus Atta have proven challenging, due in part to the extreme levels of worker polymorphism these species display, leading to disagreements about the validity of as many as five different subgenera and calling into question the monophyly of the genus. Here, we use DNA sequence information from fragments of three mitochondrial genes (COI, tRNA leucine and COII) and one nuclear gene (EF1-αF1), totaling 1070 base pairs, to reconstruct the phylogenetic relationships of Atta species using maximum parsimony, maximum likelihood and Bayesian inference techniques. Our results provide support for monophyly of the genus Atta, and suggest that the genus is divided into four monophyletic groups, which correspond to four of the five previously erected Atta subgenera: Atta sensu stricto and Archeatta, each with species composition identical to earlier proposals; Neoatta and Epiatta, with major differences in species composition from earlier proposals. The current geographic ranges of these species suggest that the historical separation of South America from Central and North America has played a role in speciation within this genus.     

The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae)

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.     

Biogeographical distribution of Hartaetosiga strains (Choanoflagellatea,Craspedida, Salpingoecidae) including morphological and transcriptomic data from a transect across the Atlantic Ocean

The genus Hartaetosiga Carr, Richter and Nitsche, 2017 comprised up to now only three species, H. gracilis (Kent) Carr, Richter, Nitsche, 2017, H. balthica (Wylezich and Karpov) Carr, Richter and Nitsche, 2017 and H. minima (Wylezich and Karpov) Carr, Richter and Nitsche, 2017. Based on distinct molecular data these species were relocated from the strictly freshwater genus Codosiga (Ehrenberg) Bütschli, 1878 to a new genus comprising brackish and marine species. During the cruise MSM82/2 across the Atlantic Ocean in 2019, surface water samples were taken from 15 stations along a transect ranging from 35°S to 23°N. We were able to isolate and cultivate 14 strains of the genus Hartaetosiga. Morphometric data showed no distinct morphological traits allowing for a species delineation, indicating a cryptic species complex within the genus. Based on cultivation, morphological data, and molecular analyses, we recorded H. gracilis for the first time from off-shelf waters of the Atlantic Ocean and could describe a new species, H. australis n. sp. This new species was recorded from sampling stations in the Southern Hemisphere only, which may indicate a potential biogeographic restriction likely caused by the Equatorial Counter Current (ECC), dividing the northern and southern surface waters.     

Molecular population genetics of a host‐associated sibling species complex of phytophagous ladybird beetles (Coleoptera: Coccinellidae: Epilachninae)

To clarify evolutionary relationships and assess the intensity and persistence of reproductive isolation because of host fidelity in three closely related host‐associated phytophagous ladybird beetles (Henosepilachna pustulosa, Henosepilachna niponica and Henosepilachna yasutomii), we determined sequences of part of the nuclear DNA internal transcribed spacer‐II (ITS‐2) region (388 bp long) for 70 individuals from seven populations, and part of the mitochondrial cytochrome c oxidase subunit I (COI) gene (985 bp long) for 280 individuals from 28 populations across the three species. We failed to detect any polymorphic sites in the ITS‐2 region. We detected 59 COI haplotypes, among which two were shared by different species. While a haplotype network and a phylogenetic gene tree of the COI haplotypes did not support monophyly for any of the three species, the results of AMOVA did not invalidate the classification of these beetles into three species. The isolation‐with‐migration analytic (IMa) test suggested that gene flow between allopatric species (i.e., H. pustulosa versus H. niponica; H. pustulosa versus H. yasutomii) was well prevented, probably because of their limited dispersal power. On the other hand, the IMa test detected a low level of unidirectional gene flow between the sympatric species H. niponica and H. yasutomii, from the former to the latter. This result was consistent with a survival rate of F1 hybrids between the two species that is higher on the host plant of H. yasutomii than on the host plant of H. niponica. High F_ST values among two sympatric and three nearly sympatric population pairs of H. niponica and H. yasutomii, however, indicated that gene flow between the two species has been quite restricted even if it has occurred. Because no reproductive barriers other than the difference in host plants is known for sympatric H. niponica and H. yasutomii, our results suggest that host differentiation and associated ecological divergence function as an effective reproductive barrier between the two species.     

Essential Oil Composition and Volatile Profile of Seven Helichrysum Species Grown in Italy

Helichrysum genus consists of about 600 species widespread throughout the world, especially in South Africa and in the Mediterranean area. In this study the aroma profile (HS‐SPME) and the EO compositions of seven Helichrysum species (H. cymosum, H. odoratissimum, H. petiolare, H. fontanesii, H. saxatile, H. sanguineum, and H. tenax) were evaluated. All the plants were grown in Italy under the same growth conditions. The volatile constituents, particularly monoterpenes, depended by the plant's genotype and ecological adaptation. This study represents the first headspace evaluation on the selected plants and the results evidenced that monoterpenes represented the main class of constituents in five of the seven species analysed (from 59.2% to 95.0%). The higher content in sesquiterpene hydrocarbons was observed in the Mediterranean species of H. sanguineum (68.0%). Only H. saxatile showed relative similar abundance of monoterpenes and sesquiterpene hydrocarbons. The essential oil composition of the majority of examined species are characterised by high percentage of sesquiterpenes (especially β‐caryophyllene and δ‐cadinene) ranging from 51.3% to 92.0%, except for H. cymosum, H. tenax, and H. sanguineum leaves where monoterpenes predominated (from 51.7% to 74.7%).     

Diversification of the Genus Anopheles and a Neotropical Clade from the Late Cretaceous

The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur.     

Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera,Phyllostomidae) with descriptions of two new species

The systematics and taxonomy of the Neotropical genus Micronycteris are not yet resolved; previous studies evidenced paraphyletic relationships, a number of potential undescribed species, and inadequate diagnostic characters. This revision focuses on the pale-bellied members of the genus using phylogenetic and morphometric tools, an increased sample size with all recognized taxa, and an expanded geographic coverage relative to prior studies. For the genetic analyses (n = 166), four molecular markers were concatenated, one mitochondrial (cytb), one nuclear (Fgb-I7), and two Y-chromosomal (DBY5 and DBY7). In the Bayesian and maximum likelihood analyses, the recognized subgenera Schizonycteris, Leuconycteris, Xenoctenes, and Micronycteris were recovered as monophyletic. The pale-bellied subgenera, Schizonycteris and Leuconycteris, were not sister clades; thus, venter coloration was not monophyletic. Leuconycteris was sister to the dark-bellied Micronycteris, and Schizonycteris was sister to the rest of the genus. Micronycteris schmidtorum was genetically defined for the first time, and it was determined all previous phylogenetic studies used a misidentified M. minuta from Bolivia. Our results showed a sister relationship between M. schmidtorum and M. brosseti, which redefines Leuconycteris. The subgenus Schizonycteris was also redefined, and it presented two well-supported clades from Central America and western Ecuador that are described as new species. Results are supported by a multivariate morphometric analyses (n = 114), karyological, and morphological comparisons. The taxonomic implications are discussed and emended diagnoses presented for the pale-bellied subgenera and for M. schmidtorum.     

Jenynsia lineata species complex,revision and new species description (Cyprinodontiformes: Anablepidae)

The Jenynsia lineata species complex comprises J. lineata from Montevideo, Uruguay and Jenynsia multidentata, from coastal basins of Brazil, Uruguay and Argentina up to 1200 m a.s.l. Taxonomic divisions within this group were tested using three different species delimitation methods, which found the two existing names to be synonyms and revealed a new cryptic species. Jenynsia darwini sp. nov. is distinguished from all congeners by having a unique combination of character states, including the shape of the dorsal postcleithrum (three times higher than wide v. less than two times higher than wide) and female colour pattern in the half of the caudal peduncle with rows of chromatophores segmented in unaligned spots (v. aligned spots forming lines). The new species also differs from J. lineata by having 26 nucleotide substitutions in the mitochondrial gene cytochrome c oxidase I (coI). Phylogenetic analysis of the genus based on morphological characters proposed by previous studies corroborates monophyly of the subgenera Plesiojenynsia and Jenynsia, with the new species being allocated to the subgenus Jenynsia as the sister group of J. lineata.     

Genetic diversity and differentiation in six species of the genus Rhinanthus (Orobanchaceae)

The intricate genus Rhinanthus L. contains many taxonomically unresolved taxa. The assessment of genetic diversity may clarify the differentiation and taxonomic relationships between species and help to determine their mating system, which is important for understanding the future prospects of populations and species. Isozymes were used to assess the mating system, genetic diversity, and differentiation in R. rumelicus, R. osiliensis, R. wagneri, R. alectorolophus, and R. angustifolius from sect. Cleistolemus and R. minor from sect. Rhinanthus. Genetic diversity at species level was found to be higher in widespread R. angustifolius and R. rumelicus compared with insular endemic R. osiliensis. Positive inbreeding coefficient revealed dominant inbreeding in endemic R. osiliensis and R. wagneri. We also detected a significant departure from Hardy–Weinberg equilibrium in some populations of R. rumelicus and R. angustifolius. The common R. alectorolophus and R. minor and several populations of R. rumelicus and R. angustifolius displayed a mixed mating mode. Six studied species divided into three distinct clusters. Rhinanthus alectorolophus was the most differentiated taxon among the investigated species. The species of sect. Cleistolemus formed two distinct groups. The first cluster consisted only of R. alectorolophus while another comprised R. rumelicus, R. osiliensis, R. wagneri, and R. angustifolius, indicating their close affinity. Thus, our isozyme results call into question the monophyly of section Cleistolemus and the taxonomic position of R. alectorolophus.     

Identification,classification and evolution of Owl Monkeys (<Emphasis Type="Italic">Aotus</Emphasis>, Illiger 1811)

Background  

Owl monkeys, belonging to the genus Aotus, have been extensively used as animal models in biomedical research but few reports have focused on the taxonomy and phylogeography of this genus. Moreover, the morphological similarity of several Aotus species has led to frequent misidentifications, mainly at the boundaries of their distribution. In this study, sequence data from five mitochondrial regions and the nuclear, Y-linked, SRY gene were used for species identification and phylogenetic reconstructions using well characterized specimens of Aotus nancymaae, A. vociferans, A. lemurinus, A. griseimembra, A. trivirgatus, A. nigriceps, A. azarae boliviensis and A. infulatus.     

Taxonomic note: Bunopithecus: A genus-level taxon for the hoolock gibbon (Hylobates hoolock)

The recent discovery that the hoolock gibbon (Hylobates hoolock [Harlan, 1834]) has a karyotype distinct from all other hylobatids provides a new and strong motive for revising gibbon taxonomy and establishing hoolocks in a separate, higher taxon. Revising Groves's taxonomy of 1972, we propose that hoolock, along with the fossil species sericus, occupy a subgenus, Bunopithecus. With the newly added taxon, the genus Hylobates would thus contain four subgenera: Bunopithecus, Hylobates, Nomascus, and Symphalangus.