Showing papers in "Zoologica Scripta in 2019"
TL;DR: The comprehensive molecular phylogeny is used to evaluate the evolution of claws in the clawless genus Apodibius and claw reduction across the Tardigrada tree of life.
Abstract: JAE/DOC Program, Grant/Award Number: JAE-DOC 2009-2012; European Marie Curie, Grant/Award Number: FP7-PEOPLE-2010-RG and PERG07-GA-2010-268289 ; Consejo Superior de Investigaciones Cientificas; FP7
53 citations
TL;DR: The case of, presumably, two consecutive Wolbachia‐mediated mitochondrial introgression events, further supports the view that infection by this endosymbiont may be frequently related to mito‐nuclear discordance in insects.
Abstract: European Regional Development Fund. Spanish Agencia Estatal de Investigacion (AEI). Grant Number: CGL2016-76322. Marie Sklodowska‐Curie. Grant Numbers: 609402-2020, 625997.
30 citations
TL;DR: The utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and the importance of a robust phylogeny for evolutionary hypothesis testing are demonstrated and novel insights may come from such approaches.
Abstract: Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, phylogenetic inference for many lineages dominated by non‐model species has not yet benefited from NGS, which can complement Sanger sequencing studies. One such lineage, whose phylogenetic relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given the lack of consensus on higher‐level relationships and the importance of a robust phylogeny for evolutionary hypothesis testing, we use a large data set comprised of hundreds of ultraconserved element (UCE) loci to infer the phylogeny of Coreoidea (excluding Stenocephalidae and Hyocephalidae), with emphasis on the families Coreidae and Alydidae. We generated three data sets by including alignments that contained loci sampled for at least 50%, 60%, or 70% of the total taxa, and inferred phylogeny using maximum likelihood and summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive phylogenetic analyses of coreoids were also re‐evaluated within our molecular phylogenetic framework. We recovered 439–970 loci per species (16%–36% of loci targeted) and combined this with previously generated UCE data for 12 taxa. All data sets, regardless of analytical approach, yielded topologically similar and strongly supported trees, with the exception of outgroup relationships and the position of Hydarinae. We recovered a monophyletic Coreoidea, with Rhopalidae highly supported as the sister group to Alydidae + Coreidae. Neither Alydidae nor Coreidae were monophyletic; the coreid subfamilies Hydarinae and Pseudophloeinae were recovered as more closely related to Alydidae than to other coreid subfamilies. Coreinae were paraphyletic with respect to Meropachyinae. Most morphological traits were homoplastic with several clades defined by few, if any, synapomorphies. Our results demonstrate the utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and highlight that novel insights may come from such approaches.
29 citations
TL;DR: The present paper integrates phylogenetic, biogeographic and paleontological data to reconstruct the evolutionary history of Neopasiphaeinae, with special emphasis on the New World taxa, relating the evolution of these bees to changes, such as the Andes uplift and expansion of open vegetation biomes.
Abstract: The biogeography of colletid bees as a whole can be explained by several South American‐Australian trans‐Antarctic interchanges. Within Colletidae, neopasiphaeine bees form a large group that has not been adequately studied, even though they are interesting both from the biogeographical viewpoint for fitting well the austral Gondwanan track and for their associations to host plants. The present paper integrates phylogenetic, biogeographic and paleontological data to reconstruct the evolutionary history of Neopasiphaeinae, with special emphasis on the New World taxa, relating the evolution of these bees to changes, such as the Andes uplift and expansion of open vegetation biomes. First, we propose a phylogenetic hypothesis for the Neopasiphaeinae using one mitochondrial and five nuclear loci. Phylogenetic relationships and divergence time estimation were simultaneously inferred in a Bayesian framework, and the tempo of neopasiphaeine diversification was investigated using lineage‐through‐time plots. The historical biogeography of neopasiphaeine bees was investigated in a likelihood framework. The clade represented by Neopasiphaeinae is strongly supported within Colletidae, and the bulk of their genera can be divided into two major sister‐clades that diverged during the Eocene: one endemic to the Australian region and the other to the Neotropical region. Divergence times among most neotropical genera of Neopasiphaeinae indicate that they differentiated and started their diversification during the Miocene. Our results depict a complex process of geographic evolution in the Neotropical clade, which probably relates to important changes in the neotropical climates and biota beginning at the Oligocene and became more marked in the Miocene. We present a scenario of the neotropical Neopasiphaeinae initially associated with areas of open vegetation in subtropical and temperate portions of South America, followed by multiple separations of lineages east and west of the Andes, and more recent occupations of habitats in tropical portions of the continent.
27 citations
TL;DR: The phylogeny indicated at least two major host switching events in the evolutionary history of the subfamily Szidatiinae which likely resulted in the transition of these parasites from birds to fish and snakes.
Abstract: The Cyathocotylidae is a globally distributed family of digeneans parasitic as adults in fish, reptiles, birds, and mammals in both freshwater and marine environments. Molecular phylogenetic analysis of interrelationships among cyathocotylids is lacking with only a few species included in previous studies. We used sequences of the nuclear 28S rRNA gene to examine phylogenetic affinities of 11 newly sequenced taxa of cyathocotylids and the closely related family Brauninidae collected from fish, reptiles, birds, and dolphins from Australia, Southeast Asia, Europe, North America and South America. This is the first study to provide sequence data from adult cyathocotylids parasitic in fish and reptiles. Our analyses demonstrated that the members of the genus Braunina (family Brauninidae) belong to the Cyathocotylidae, placing the Brauninidae into synonymy with the Cyathocotylidae. In addition, our DNA sequences supported the presence of a second species in the currently monotypic Braunina. Our phylogeny revealed that Cyathocotyle spp. from crocodilians belong to a separate genus (Suchocyathocotyle, previously proposed as a subgenus) and subfamily (Suchocyathocotylinae subfam. n.). Morphological study of Gogatea serpentum indicum supported its elevation to species as Gogatea mehri. The phylogeny did not support Holostephanoides within the subfamily Cyathocotylinae; instead, Holostephanoides formed a strongly supported clade with members of the subfamily Szidatiinae (Gogatea and Neogogatea). Therefore, we transfer Holostephanoides into the Szidatiinae. DNA sequence data revealed the potential presence of cryptic species reported under the name Mesostephanus microbursa. Our phylogeny indicated at least two major host switching events in the evolutionary history of the subfamily Szidatiinae which likely resulted in the transition of these parasites from birds to fish and snakes. Likewise, the transition to dolphins by Braunina represents another major host switching event among the Cyathocotylidae. In addition, our phylogeny revealed more than a single transition between freshwater and marine environments demonstrated in our dataset by Braunina and some Mesostephanus.
26 citations
TL;DR: Investigation of the genetic structure and diversity of seven hyalid species inhabiting the Macaronesian, European and Moroccan Atlantic coasts, with a focus on the genetic differentiation between island and Continental populations indicates distinct evolutionary and diversification patterns among Hyalidae species.
Abstract: Sequence data and specimen metadata were uploaded in the project “Hyalidae DiverseShores” (DSHYA; https://doi.org/10.5883/DS-HYALIDNE) within BOLD (Ratnasingham & Hebert, 2007) and made available in GenBank under accession numbers MK216332–MK216495. Specimens used (and conspecific specimens sampled in the same locations) were deposited at CESAM at the University of Aveiro, Portugal, and may be available upon request.
24 citations
TL;DR: The results suggest that several desirable phylogenetic qualities were observed when allowing ≥60% missing data per SNP, however, at the highest missing data thresholds, there are differences in performance between high‐ and mixed‐weight DNA extraction samples, which may indicate there are trade‐offs to consider when using degraded genomic template with RADseq protocols.
Abstract: Restriction site‐associated DNA sequencing (RADseq) has emerged as a useful tool in systematics and population genomics. A common feature of RADseq data sets is that they contain missing data that arise from multiple sources including genealogical sampling bias, assembly methodology and sequencing error. Many RADseq studies have demonstrated that allowing sites (single nucleotide polymorphisms, SNPs) with missing data can increase support for phylogenetic hypotheses. Two non‐mutually exclusive explanations for this observation are that (a) larger data sets contain more phylogenetic information; and (b) excluding missing data disproportionally removes sites with the highest mutation rates, causing the exclusion of characters that are likely variable and informative. Using a RADseq data set derived from the East African banana frog, Afrixalus fornasini (up to 1.1 million SNPs), we found that missing data thresholds were positively correlated with the proportion of parsimony‐informative sites and mean branch support. Using three proxies for estimating site‐specific rate, we found that the most conservative missing data strategies excluded rapidly evolving sites, with four‐state sites present only when allowing ≥60% missing data per SNP. Topological similarity among estimated phylogenies was highest for the data sets with ≥60% missing data per SNP. Our results suggest that several desirable phylogenetic qualities were observed when allowing ≥60% missing data per SNP. However, at the highest missing data thresholds (80% and 90% missing data per SNP), we observed differences in performance between high‐ and mixed‐weight DNA extraction samples, which may indicate there are trade‐offs to consider when using degraded genomic template with RADseq protocols.
24 citations
Swedish University of Agricultural Sciences1, National Museum of Natural History2, National University of Patagonia San Juan Bosco3, Spanish National Research Council4, Linnaeus University5, University of São Paulo6, University of Bonn7, Moscow State University8, Far Eastern Federal University9, Russian Academy of Sciences10, Weber State University11, Harvard University12, University of Magdalena13, University of Alcalá14, University of Oregon15, Hokkaido University16, University of Toronto17, Royal Ontario Museum18, University of Puget Sound19, Ocean University of China20, University of Gothenburg21, Virginia Commonwealth University22
TL;DR: The ranks Anopla and Enopla are eliminated and the following system of the Nemertea phylum is implemented and genus Hubrechtella is transferred from class Palaeonemertea to the class Pilidiophora.
Abstract: Dear Editor, Nemertean classification has closely followed Stiasny‐ Wijnhoff’s scheme (1936) that was based on Schultze’s (1851) division of the taxon into the two classes Anopla and Enopla. In August 2018, the 9th International Conference of Nemertean Biology took place in the Wadden Sea Station of the Alfred Wegener Institute in List auf Sylt, Germany. At this meeting, the community reached consensus to revise nemertean taxonomy at the class level, based on the compiled evidence from studies on nemertean systematics published in the last 15 years (Andrade et al., 2014, 2012 ; Thollesson & Norenburg, 2003). Previous classifications (e.g., Stiasny‐ Wijnhoff, 1936) are not based on phylogenetic grounds, and the use of these names is therefore nowadays not wholly informative. With the purpose of facilitating the practical use of the nemertean taxonomy and also making nemertean taxonomy reflect a wealth of more recent information, we conclude that the ranks Anopla and Enopla should be eliminated with the following argumentation: “Enopla” has for long held no more information than the name “Hoplonemertea”. “Anopla” is paraphyletic and the name usually corresponds to the following traits: (a) not bearing stylet; and (b) mouth and proboscis having separate openings. This information is equally well presented in a system that also bears information on natural groups. The names “Anopla” and “Enopla” are hence dismissed and the following system of the Nemertea phylum is implemented: Class: Palaeonemertea Currently no Orders Class: Pilidiophora Order: Heteronemertea Class: Hoplonemertea Order: Monostilifera Order: Polystilifera The changes do not affect lower levels of taxonomy, but in accordance with Thollesson and Norenburg (2003), who first presented Pilidiophora, genus Hubrechtella is transferred from class Palaeonemertea to the class Pilidiophora.
22 citations
TL;DR: In this article, the authors reconstructed several two-marker (mtDNA cytochrome c oxidase subunit I-COI and NADH dehydrogenase sub-unit 1-ND1) phylogenies with newly collected specimens and all previously available sequences covering most species within Quadrula sensu lato.
Abstract: Freshwater mussels (Bivalvia, Unionidae) have suffered strong declines over the last century. High morphological plasticity of Unionidae causes disturbances in their systematics and taxonomy, hampering conservation efforts. Species that have historically been placed under the North American genus Quadrula have suffered from numerous taxonomic and species delineation problems since its inception. Four genera are presently recognized within Quadrula sensu lato, that is, Cyclonaias, Quadrula, Theliderma and Tritogonia, but their phylogenetic basis remains incompletely tested. In the present study, we reconstructed several two‐marker (mtDNA cytochrome c oxidase subunit I—COI and NADH dehydrogenase subunit 1—ND1) phylogenies with newly collected specimens and all previously available sequences covering most species within this group. We then delineated the species within the group using an integrative approach with the application of molecular statistical methods, morphometric (Fourier Shape) analyses and geographic distribution data. Four clades corresponding to these genera were consistently recovered in all phylogenies. To validate the generic status of these clades, molecular analyses were complemented with morphological, anatomical and ecological data compiled from the literature. Several revisions are here proposed to the current systematics and taxonomy of these genera, including the synonymization of Cyclonaias asperata under Cyclonaias kieneriana; the inclusion of Quadrula apiculata and Quadrula rumphiana under Quadrula quadrula; the placement of Quadrula nobilis under Tritogonia; and finally the separation of the Mobile River basin populations of Theliderma metanevra as a new species, that is, Theliderma johnsoni n. sp. The conservation implications of the proposed changes are then discussed.
22 citations
TL;DR: It is found that species in the families Diplogyniidae and Parasitidae have retained the ancestral mt genome organization of arthropods, which is in stark contrast to the highly rearranged mt genomes in the Phytoseiidae species.
Abstract: Mesostigmata is an extremely diverse group of mites with more than 11,000 described species in 109 families. The complete mitochondrial (mt) genomes of five species of mesostigmatid mites from three families (Varroidae, Ologamasidae, Phytoseiidae) have been reported previously; all of them are rearranged or highly rearranged in gene order. However, it is unclear when mt genome reorganization occurred and how common it is in mesostigmatid mites. We sequenced the mt genomes of ten species of mesostigmatid mites from five more families (Blattisociidae, Diplogyniidae, Laelapidae, Macrochelidae, Parasitidae). We found that species in the families Diplogyniidae and Parasitidae have retained the ancestral mt genome organization of arthropods, which is in stark contrast to the highly rearranged mt genomes in the Phytoseiidae species. As in the Varroidae and Ologamasidae species, the mt genomes of the Blattisociidae, Macrochelidae and Laelapidae species are also rearranged but are less rearranged than in the Phytoseiidae species. Each of the six mesostigmatid families that have rearranged mt genomes is characterized by unique gene order not seen in other mesostigmatid families. Furthermore, the mt genome organization also differs among three genera of the Phytoseiidae, between two genera of the Laelapidae, and among three Macrocheles species of the Macrochelidae. Our results indicate that: (a) the most recent common ancestor of mesostigmatid mites likely retained the ancestral mt genome organization of arthropods; and (b) mt genome organization characterizes various lineages of mesostigmatid mites and provides a valuable source of information for understanding their phylogeny and evolution.
21 citations
TL;DR: Diet specialization, radular morphology and the type of protoconch as well as conotoxin diversity were mapped onto the reconstructed mt phylogeny, and a chronogram dating mayor cladogenetic events within the group was also reconstructed.
Abstract: Understanding the relative role of different evolutionary processes leading to the extraordinary morphological, ecological and species diversity of cone snails requires a robust phylogeny, which thus far has been elusive. Here, we constructed a mitochondrial (mt) genome data set, which included four newly sequenced mt genomes, 25 publicly available mt genomes and 24 data sets with all mt protein‐coding and rRNA genes assembled from venom gland transcriptomes. In total, we analysed 42 different species representing 27 genera of cone snails, that is, about one third of the generic diversity of the group. In addition, we used the RNA‐Seq reads to assemble 21 nuclear genes, which were concatenated in a nuclear data set. Finally, a combined data set including mt and nuclear genes was also constructed. The three data matrices were analysed with probabilistic methods, site‐homogeneous and site‐heterogeneous models, and with protein‐coding genes both at the amino acid and nucleotide levels. Diet specialization, radular morphology and the type of protoconch (paucispiral or multispiral indicating lecithotrophic or planktonic larvae, respectively) as well as conotoxin diversity were mapped onto the reconstructed mt phylogeny, and a chronogram dating mayor cladogenetic events within the group was also reconstructed.
TL;DR: The phylogeny of mylodontid sloths has recently been the subject of multiple studies, and a new and detailed phylogenetic analysis is conducted, after adding new characters and taxa previously unexplored from a phylogenetic point of view to represent the first exhaustive phylogenetic study on the MyLodontidae that incorporates features coded for the entire skeleton.
Abstract: Fil: Boscaini, Alberto. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Mendoza. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales. Provincia de Mendoza. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales. Universidad Nacional de Cuyo. Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales; Argentina
TL;DR: cies delimitation using mitochondrial data strongly supports the presence of two sympatric species within C. alipioi in southeastern Brazil despite limited morphological variation and conserved chromosomal patterns and provides a framework to further the study of systematics and evolution within Characidium.
Abstract: Neotropical darters of the genus Characidium have a complex systematic history with several examples of sympatry throughout their distribution range in Neotropical freshwaters. Although various species within the genus have been used as models to investigate chromosomal evolution and biogeography, species boundaries and relationships still remain uncertain. Here, we use mitochondrial DNA sequences to perform species delimitation analyses within Characidium and test previous hypotheses of species richness within the Characidium zebra complex and among sympatric morphotypes of C. alipioi. Results indicate high genetic distances within tested species complexes and revealed the presence of strongly supported lineages such as the large C. lauroi group from southeastern Brazil. This suggests that the evolutionary history of these groups may be correlated with biogeographic history. Analyses also reveal that three geographically isolated populations of C. zebra represent a single species, leading us to reject prior hypothesis of multiple species. Species delimitation using mitochondrial data strongly supports the presence of two sympatric species within C. alipioi in southeastern Brazil despite limited morphological variation and conserved chromosomal patterns. These results provide a framework to further the study of systematics and evolution within Characidium.
TL;DR: The findings imply that researchers should use the number of SSP more carefully in comprehensive studies, and maintain and use the rank subspecies in order to provide a stronger status for the species rank, and avoid taxonomic inflation.
Abstract: Subspecies richness (average number of subspecies per species = SSP/SP) has traditionally been explained by niche breadth, characteristics of the preferred habitat (“habitat hypothesis”), dispersal ability, range size (“range size hypothesis”), etc. However, in several invertebrate groups, there are striking differences between SSP/SP across families, which cannot be explained using classic arguments, and we might assume some hidden factor in the background. For example, some families of terrestrial molluscs, that possess conspicuously more subspecies than others, have higher degree of morphological complexity (shell size, number of diagnosable shell characters), for which we propose the “artefact hypothesis.” According to this, morphological complexity plays an important role in taxonomists' subspecies recognition. We used shell size, number of characters mentioned in species descriptions and area extent in six European land snail families, and habitat characteristics (rock‐dwelling vs. non‐rock‐dwelling) in one largest European snail families (Clausiliidae) to test our hypothesis. We found that all three factors (range size, morphological complexity and habitat type) correlated positively with the SSP/SP ratio. Although the generality of our findings has to be tested in other invertebrate phyla, we provide examples of striking differences between SSP/SP ratios in butterflies (Lepidoptera) and beetles (Coleoptera) as well. Our findings imply that researchers (a) should use the number of SSP more carefully in comprehensive studies, and (b) should maintain and use the rank subspecies in order to provide a stronger status for the species rank, and avoid taxonomic inflation. Furthermore, the subspecies rank might be more useful for “cryptic species” (clades that are indistinguishable morphologically) than species.
TL;DR: The analyses indicate that Laniidae as currently delimited is not monophyletic, as the genus Eurocephalus is not closely related to the remaining species, and it is proposed that the two species currently assigned to the monotypic genera Urolestes and Corvinella are part of the same clade as the Lanius species.
Abstract: Diversification of avifaunas associated with savannah and steppes appears to correlate with open habitats becoming available, starting in the Miocene. Few comparative analyses exist for families fo ...
TL;DR: A complete set of pika taxa, belonging to the subgenus Ochotona, was studied using craniometric and multilocus genetic analyses and new subspecies was found within O. thibetana, indicating that mitochondrial DNA cannot be used for species identification in thissubgenus.
Abstract: A complete set of pika taxa, belonging to the subgenus Ochotona, was studied using craniometric and multilocus genetic analyses. We examined 1,007 skulls, covering the entire distribution range of the subgenus, as well as the mitochondrial COI gene and three nuclear introns in 31 specimens, representing nearly all taxa in question. An additional set of 167 COI gene sequences and 357 cytb gene sequences was analysed to enlarge the geographical extent of genetic data and to compare the results with previous publications. We found that the subgenus consists of eight species. One of them, Ochotona morosa, is elevated to the full species rank for the first time. The name of this species is given preliminarily and should be studied additionally. Several cases of interspecies hybridisation were found, which indicates that mitochondrial DNA cannot be used for species identification in this subgenus. Taxon Ochotona qionglaiensis, which was recently described as a separate species, represents a relic mitochondrial lineage of Ochotona thibetana. Another recently described species, Ochotona yarlungensis, is a Nubra pika with its native mitochondrial DNA, firstly found for this species. Intraspecies variation was analysed for several species for the first time. Thus, new subspecies (Ochotona thibetana fengii ssp. n.) was found within O. thibetana.
TL;DR: It is proposed that the Wuyi disjunction of the Chestnut‐vented Nuthatch was most likely due to recent range expansion from south‐western China during the glacial period, followed by postglacial range retraction.
Abstract: Pleistocene climatic oscillations have played an important role in shaping many species’ current distributions. In recent years, there has been increasing interest in studying the effects of glacial periods on East Asian birds. Integrated approaches allow us to study past distribution range changes due to Pleistocene glaciation, and how these changes have affected current population genetic structure, especially for species with unusual distribution patterns. The Wuyi disjunction is the disjunct distribution of birds between the Wuyi Mountains in south‐eastern China and south‐western China. Although several species exhibit the Wuyi disjunction, the process behind this unusual distribution pattern has remained relatively unstudied. Therefore, we used the Chestnut‐vented Nuthatch Sitta nagaensis as a model species to investigate the possible causes of the Wuyi disjunction. Based on phylogenetic analyses with three mitochondrial and six nuclear regions, the Wuyi population of the Chestnut‐vented Nuthatch was closely related to populations in mid‐Sichuan, from which it diverged approximately 0.1 million years ago, despite the long geographical distance between them (over 1,300 km). In contrast, geographically close populations in mid‐ and southern Sichuan were genetically divergent from each other (more than half a million years). Ecological niche modelling suggested that the Chestnut‐vented Nuthatch has experienced dramatic range expansions from Last Interglacial period to Last Glacial Maximum, with some range retraction following the Last Glacial period. We propose that the Wuyi disjunction of the Chestnut‐vented Nuthatch was most likely due to recent range expansion from south‐western China during the glacial period, followed by postglacial range retraction.
TL;DR: A molecular phylogeny is generated that includes four previously unsampled Mesoamerican genera and nine species endemic to that region and more completely recognizes the suprageneric diversity of the Ambleminae.
Abstract: Evolutionary and ecological hypotheses of the freshwater mussel subfamily Ambleminae are intensely geographically biased—a consequence of the complete exclusion of Mesoamerican taxa in phylogenetic reconstructions of the clade. We set out to integrate a portion of the Mesoamerican freshwater mussel assemblage into existing hypotheses of amblemine classification and evolution by generating a molecular phylogeny that includes four previously unsampled Mesoamerican genera and nine species endemic to that region. Given the traditionally hypothesized affinity to Nearctic mussels and the understanding that classification should reflect common ancestry, we predicted that (a) Mesoamerican genera would be recovered as members of the recognized tribes of the Ambleminae, and (b) genera would be supported as monophyletic. The mutilocus phylogeny (COI + 28S + 16S) reported herein does not fully support either of those hypotheses. Neither Cyrtonaias nor Psorula were supported as monophyletic and we predict several other Mesoamerica genera are also non‐monophyletic. The reconstructed phylogeny recovered four independent lineages of Mesoamerican freshwater mussels and these clades are distributed across the phylogeny of the Ambleminae, including the tribe Quadrulini (Megalonaias), Lampsilini (two lineages: Cyrtonaias explicata/Sphenonaias microdon, and Pachynaias), and a previously unrecognized, exclusively Mesoamerican and Rio Grande clade consisting of the genera Psoronaias, Psorula and Popenaias. The latter clade possesses several morphological characteristics that distinguish it from its sister taxon, tribe Lampsilini, and we recognize this newly identified Mesoamerican clade as a fifth tribe of the Ambleminae attributable to the Popenaiadini Heard & Guckert, 1970. This revised classification more completely recognizes the suprageneric diversity of the Ambleminae.
TL;DR: The phylogeny of Cyclops (~30 spp.), a predominantly Palearctic cold‐adapted genus, was reconstructed based on morphological and molecular characters, suggesting two independent invasions into North America via the Bering Land Bridge from Siberia to Alaska.
Abstract: The phylogeny of Cyclops (~30 spp.), a predominantly Palearctic cold‐adapted genus, was reconstructed based on morphological and molecular characters. The morphological analysis used extensive taxon sampling from the entire Holarctic range of the genus and included 53 morphological characters. Polymorphic traits were coded by the “unordered,” “unscaled” and “scaled” methods; maximum parsimony criterion was applied in tree building. Molecular phylogenetic reconstructions utilized partial nuclear 18S and 28S ribosomal genes, mitochondrial cytochrome oxidase I and complete internal transcribed spacer regions I and II, albeit with limited taxon sampling. Bayesian inference and maximum likelihood were used in these tree reconstructions. The molecular characters were used both in combination with morphology and as an independent test of the basal relationships inferred from morphology. Monophyly of the genus received strong support in both the morphological and molecular phylogenies; the basal relationships remain unresolved. The morphology‐based phylogenies, along with the geographic distribution patterns and ecological traits, supported monophyly of the ankyrae−ladakanus clade, scutifer‐clade (C. scutifer, C. jashnovi, C. columbianus), kolensis‐clade (C. kolensis, C. kikuchii, C. vicinus, C. furcifer, C. insignis, C. alaskaensis), abyssorum‐clade (C. abyssorum s. str., C. abyssorum larianus, C. ricae, C. sevani) and divergens‐clade (South Carpathian “Cyclops sp. Y,” C. mauritaniae, C. divergens, C. bohater, C. lacustris). Relationships among European and North American populations of C. scutifer and C. columbianus based on partial sequences of the 12S mitochondrial gene show C. scutifer to be paraphyletic, suggesting two independent invasions into North America via the Bering Land Bridge from Siberia to Alaska.
TL;DR: The first large‐scale, total‐evidence phylogeny of the owlflies (Neuroptera, Ascalaphidae) is presented and a new subfamilial classification based on these results is proposed, as Myrmeleontoidea, in order to accommodate much‐needed taxonomic and nomenclatural restructuring anticipated to occur within the AsCalaphidae in the future.
Abstract: The first large‐scale, total‐evidence phylogeny of the owlflies (Neuroptera, Ascalaphidae) is presented. A combined morphological and molecular dataset was analysed under several analytical regimes for 76 exemplars of Myrmeleontiformia (Psychopsidae, Nymphidae, Nemopteridae, Myrmeleontidae, Ascalaphidae), including 57 of Ascalaphidae. At the subordinal level, the families were recovered in all analyses in the form Psychopsidae + (Nymphidae + (Nemopteridae + (Myrmeleontidae + Ascalaphidae). In the DNA‐only maximum‐likelihood analysis, Ascalaphidae were recovered as paraphyletic with respect to the Myrmeleontidae and the tribe Ululodini. In both the parsimony and Bayesian total‐evidence analyses, however, the latter with strong support, traditional Ascalaphidae were recovered as monophyletic, and in the latter, Stilbopteryginae were placed as the immediate sister group. The long‐standing subfamilies Haplogleniinae and Ascalaphinae were not recovered as monophyletic in any analysis, nor were several of the included tribes of non‐ululodine Ascalaphinae. The Ululodini were monophyletic and well supported in all analyses, as were the New World Haplogleniinae and, separately, the African/Malagasy Haplogleniinae. The remaining Ascalaphidae, collectively, were also consistently cohesive, but included a genus that until now has been placed in the Haplogleniinae, Protidricerus. Protidricerus was discovered to express a well‐developed pleurostoma, a feature previously only encountered in divided‐eye owlflies. The feature traditionally used to differentiate the Haplogleniinae and Ascalaphinae, the entire or divided eye, can no longer be regarded as a spot‐diagnostic synapomorphy to separate these groups within the family. A new subfamilial classification based on these results is proposed and includes the following five subfamilies: Albardiinae, Ululodinae, Haplogleniinae, Melambrotinae and Ascalaphinae. In addition, the monophyletic containing group (Myrmeleontidae + (Palparidae + (Stilbopterygidae + Ascalaphidae))) is elevated to the rank of superfamily, as Myrmeleontoidea, in order to accommodate much‐needed taxonomic and nomenclatural restructuring anticipated to occur within the Ascalaphidae in the future. A list of genera included in each subfamily of Ascalaphidae is provided.
TL;DR: The results revealed that the Barbus fishes of the mid‐Adriatic region of Europe have a complex pattern of local endemism and should be managed by treating them as unique evolutionary units and ceasing translocations of all BarbUS fishes between river basins.
Abstract: © 2019 Royal Swedish Academy of Sciences Italian freshwaters are highly biodiverse, with species present including the native fishes Barbus plebejus and Barbus tyberinus that are threatened by habitat alteration, fish stocking and invasive fishes, especially European barbel Barbus barbus. In central Italy, native fluvio-lacustrine barbels are mainly allopatric and so provide an excellent natural system to evaluate the permeability of the Apennine Mountains. Here, the morphologic and genetic distinctiveness was determined for 611 Barbus fishes collected along the Padany–Venetian (Adriatic basins; PV) and Tuscany–Latium (Tyrrhenian basins; TL) districts. Analyses of morphological traits and mitochondrial DNA sequence data explored the natural and anthropogenic factors that have shaped their distribution ranges. Over 100 alien B. barbus were recorded in the Tiber basin (TL district) and Metauro basin (PV district). Comparisons of genetic and morphometric data revealed that morphometric data could identify alien B. barbus from native Barbus, but could not differentiate between B. tyberinus and B. plebejus. Genetic analyses revealed ~50 D-loop mtDNA haplotypes and identified a distinct Barbus lineage present only in the Vomano River at the southern boundary of PV district. Demographic expansion and molecular variance analyses revealed a lack of geographic structuring across the sampling regions. While the contemporary B. plebejus distribution has been driven primarily by anthropogenic fish translocations, the dispersal of B. tyberinus has been via natural dispersion, including their crossing of the Apennine Mountains via temporary river connectivity. The results also revealed that the Barbus fishes of the mid-Adriatic region of Europe have a complex pattern of local endemism. To conserve these patterns of genetic uniqueness, especially in the mid-Adriatic basins, Barbus fishes should be managed by treating them as unique evolutionary units and ceasing translocations of all Barbus fishes between river basins.
TL;DR: The morphological and phylogenetic affinities of Tethytrygon gen. n.
Abstract: The Eocene whiptail stingrays of the family Dasyatidae from the Bolca Lagerstatte, NE Italy, are revised herein in detail. The analysis of the anatomical and morphometric features allows us to identify the species "Dasyatis" zigni (Molin, 1861) as a junior synonym of "D." muricatus (Volta, 1796), and to assign it to the new genus Tethytrygon gen. n. This new taxon exhibits a unique combination of features (e.g., rhombic disc wider than long, elongated tail folds fail to reach the tip of the tail, thorns absent, single serrated tail sting, "caniniform" teeth on upper jaw, tooth crown ornamentation absent, 175-179 vertebrae, 108-117 pectoral radials, 24-27 pelvic radials and other features of clasper anatomy) that clearly support its attribution to the subfamily Neotrygoninae of the stingray family Dasyatidae. The morphological and phylogenetic affinities of Tethytrygon gen. n. with the living neotrygonines (Neotrygon and Taeniura) suggest a close association of this taxon with the tropical shallow-water habitats hypothesized for the Bolca palaeoenvironment during the early Eocene. Moreover, the analysis of the fossil occurrences of the neotrygonines provides new insights into the role of the Tethys for the origin and evolutionary history of certain whiptail stingrays.
TL;DR: A robust phylogenetic component is found in these characteristics, where strongly supported clades are recovered: prior to the onset of the Early Miocene, a triadal and tricolour tail clade composed of species from South America, and a second clade dating to the Middle‐Late‐ Miocene with monadal and bicolour tails widely distributed from North to South America.
Abstract: In this study, we analyse New World coral snakes in a phylogenetic framework based upon an increased molecular data set, including novel sequences for the only two sympatric species known from an island (Trinidad, West Indies). Their presence in Trinidad and absence in Tobago offers a unique system to study the phylogeography of the region. We assess the tempo and mode of colonisation of Micrurus on the island, in addition to discussing the phylogenetic relationships for the genus Micrurus concerning two phenotypic traits, body and tail banding patterns. These relationships are analysed for the first time on statistical coalescent phylogeographic discrete ancestral reconstruction. We find a robust phylogenetic component in these characteristics, where strongly supported clades are recovered: prior to the onset of the Early Miocene, a triadal and tricolour tail clade composed of species from South America, and a second clade dating to the Middle‐Late‐ Miocene with monadal and bicolour tails widely distributed from North to South America. The divergence between clades dates to the Oligocene and suggests an ancient pre‐isthmus divergence supporting the arrival of the triadal clade into South America, before the connection between Central and South America was established. We find the two coral snakes present in the West Indies, M. diutius and M. circinalis, belong to the triadal and monadal clades, respectively. Guyana and Trinidad Micrurus diutius share the same haplotypes suggesting a Late Pleistocene–Holocene vicariance when sea level rises separated Trinidad from the mainland. A second lineage of diutius‐like snakes is present in Guyana and is confirmed as M. lemniscatus which is assigned as a voucher and restricts the type locality for M. lemniscatus.
TL;DR: High levels of genetic variation are shown between regional populations of this non‐spitting cobra, including the north‐eastern, north‐central and southern regions, in addition to a population on Pha‐ngan Island, 150 km offshore from the southern peninsula.
Abstract: South‐East Asia has an exceptionally high diversity of snakes, with more than 250 snake species currently recorded from Thailand. This diversity likely reflects the diverse range of geographical and climatic conditions under which they live, but the evolutionary history and population genetics of many snake species in South‐East Asia have been little investigated in comparison with morphological studies. Here, we investigated genetic variation in the monocled cobra, Naja kaouthia, Lesson, 1831, across its distribution range in Thailand using mitochondrial DNA (cytochrome b, control region) for ~100 individuals and the nuclear DNA gene (C‐mos) for a small subset. Using population genetic and phylogenetic methods, we show high levels of genetic variation between regional populations of this non‐spitting cobra, including the north‐eastern, north‐central and southern regions, in addition to a population on Pha‐ngan Island, 150 km offshore from the southern peninsula. Moreover, inclusion of the north‐eastern population renders N. kaouthia paraphyletic in relation to other regional Naja species. The north‐eastern population is therefore probably specifically distinct. Given that these cobras are otherwise undifferentiated based on colour and general appearance to the “typical” cobra type of this region, they would represent a cryptic species. As has been shown in other animal groups from Thailand, it is likely that the geographical characteristics and/or tectonic alteration of these regions have facilitated high levels of population divergence of N. kaouthia in this region. Our study highlights the need for dense sampling of snake populations to reveal their systematics, plan conservation and facilitate anti‐snake venom development.
TL;DR: A total evidence phylogeny that places fossil flatfishes among extant lineages is constructed and finds polyphyly or paraphyly of two flatfish families, the Paralichthyidae and the Rhombosoleidae, and supports the creation of two additional families to resolve their non‐monophyletic status.
Abstract: Flatfishes (Pleuronectiformes) are a species‐rich and distinct group of fishes characterized by cranial asymmetry. Flatfishes occupy a wide diversity of habitats, including the tropical deep‐sea and freshwaters, and often are small‐bodied fishes. Most scientific effort, however, has been focused on large‐bodied temperate marine species important in fisheries. Phylogenetic study of flatfishes has also long been limited in scope and focused on the placement and monophyly of flatfishes. As a result, several questions in systematic biology have persisted that molecular phylogenetic study can answer. We examine the Pleuronectoidei, the largest suborder of Pleuronectiformes with >99% of species diversity of the order, in detail with a multilocus nuclear and mitochondrial data set of 57 pleuronectoids from 13 families covering a wide range of habitats. We combine the molecular data with a morphological matrix to construct a total evidence phylogeny that places fossil flatfishes among extant lineages. Utilizing a time‐calibrated phylogeny, we examine the timing of diversification, area of origin and ancestral temperature preference of Pleuronectoidei. We find polyphyly or paraphyly of two flatfish families, the Paralichthyidae and the Rhombosoleidae, and support the creation of two additional families—Cyclopsettidae and Oncopteridae—to resolve their non‐monophyletic status. Our findings also support the distinctiveness of Paralichthodidae and refine the placement of that lineage. Despite a core fossil record in Europe, the observed recent diversity of pleuronectoids in the Indo‐West Pacific is most likely a result of the Indo‐West Pacific being the area of origin for pleuronectoids and the ancestral temperature preference of flatfishes is most likely tropical.
TL;DR: Comparison of the results with the phylogeographic history of other woodpeckers, suggests that sympatric species with similar life‐histories might have idiosyncratic phyloGeographic patterns probably resulting from different ecological requirements or historic stochasticity.
Abstract: Population divergence could be strongly affected by species’ ecology and might not be a direct response to climate‐driven environmental change. We tested this in the middle spotted woodpecker (Dendrocoptes medius), a non‐migratory, low‐dispersal habitat specialist associated with old deciduous forests of the Western Palearctic. We present the first phylogeographic study of this species integrating genetic data (three mitochondrial loci, one autosomal and one Z‐linked intron) with species distribution modelling. Based on this species’ ecology, we predicted that the middle spotted woodpecker could have colonized its current range from multiple Last Glacial Maximum (LGM) refugia and that strongly structured populations could be expected. Indeed, we discovered a strong genetic divergence between Asian and European populations, with a split estimated at around one million of years ago. This was surprising given only slight intraspecific variation in plumage and morphology. Although there was no significant phylogeographic structure within the Asian and European groups, we cannot exclude the possibility of multiple refugia within either group during the LGM. This has to be further investigated with more extensive geographic sampling and larger number of variable independently evolving markers. Future studies should also investigate potential differences in vocalizations and ecology between the two groups. Lineages showing similar level of genetic differentiation including woodpeckers are often treated as species‐level taxa. Comparison of our results with the phylogeographic history of other woodpeckers, suggests that sympatric species with similar life‐histories might have idiosyncratic phylogeographic patterns probably resulting from different ecological requirements or historic stochasticity.
TL;DR: The phylogeography and social structure of the narrow endemic velvet worm species Opisthopatus amaxhosa were investigated by conducting fine‐scale sampling in its distribution range in the Eastern Cape province of South Africa, providing evidence for a novel species that is present at a fine scale.
Abstract: The phylogeography and social structure of the narrow endemic velvet worm species Opisthopatus amaxhosa were investigated by conducting fine‐scale sampling in its distribution range in the Eastern Cape province of South Africa. In addition, and as part of larger grant on forest biodiversity, Opisthopatus specimens sampled at localities not included during a recent evaluation of the genus were included in a new phylogeny. A total of 89 specimens from 18 sample localities were collected at three forest patches for O. amaxhosa samples, while an additional six Opisthopatus sample localities were included. For O. amaxhosa, we sequenced the COI locus for all specimens, while a subset of specimens was sequenced for two nuclear loci, 18S rRNA and the fushi tarazu intron (FTz). Phylogenetic analyses using maximum likelihood and Bayesian inferences of the latter species revealed the presence of two highly divergent clades, characterised by marked uncorrected sequence divergence values. In addition, these two clades did not share any maternal haplotypes, were characterised by high FST values and fixed nuclear difference for the 18S rRNA locus, while the FTz intron was genetically invariant. Furthermore, the application of scanning electron microscopy between the two genetically divergent clades also revealed the presence of fixed ventral and dorsal scale numbers. Collectively, this provides evidence for a novel species that is present at a fine scale. Divergence time estimations suggest that the two clades diverged during the late and early Pleistocene with climatic cycling potentially causal to the fragmentation. The social structure was male‐biased, and samples from the same logs were not always genetically identical. At the broader scale, the inclusion of new specimens within Opisthopatus revealed no novel lineages. Fine‐scale sampling appears more important to detect alpha taxonomic diversity compared to broadscale sampling.
TL;DR: The resulting tree topologies imply the need for a thorough revision of tribal classification within Melolonthinae lineages to accommodate the polyphyly of Tanyproctini, which appears to be mainly based on presumably plesiomorphic characters.
Abstract: Tanyproctini (Melolonthinae) is a large group of chafers within the pleurostict Scarabaeidae that shows an enormous morphological diversity and variation. However, their morphology based definition appears to be mainly based on presumably plesiomorphic characters. Here, we investigate the phylogeny of this interesting lineage with a three‐gene data set using partial gene sequences of 28S rRNA, cytochrome c oxidase I (cox1) and 16S rRNA (rrnL). Our data set comprised 191 species of all major lineages of pleurostict scarabs. Combined analyses of the 2,070 base pairs alignment with maximum‐likelihood and Bayesian tree inference always recovered Tanyproctini to be highly polyphyletic. Tests of an alternative topology with constrained monophyly of Tanyproctini using CONSEL and IQ‐TREE were not found to be more likely than the unconstrained tree topology. Instead, Tanyproctini was split into six independent lineages under the current taxon sampling that were scattered throughout diverse parts of the pleurostict tree. The fact that numerous smaller chafer lineages exist beside several evolutionary successful and large lineages, highlights the complexity of the pleurosticts’ evolutionary history. The resulting tree topologies imply the need for a thorough revision of tribal classification within Melolonthinae lineages to accommodate the polyphyly of Tanyproctini. However, a revision of classification would be premature due to low support of most relevant branches, instable tree topologies among different tree searches, and due to a still very incomplete representation of Tanyproctini lineages.
TL;DR: This study represents the first integrative analysis of a poorly known evolutionary radiation of one of the most widespread SA fossorial snakes and describes hemipenial ornamentation, a potential source of systematic and taxonomic characters in Typhlopinae.
Abstract: Typhlopidae is the most diverse family of Scolecophidia, with 269 species. Amerotyphlops was recently erected within subfamily Typhlopinae and comprises fifteen species distributed from Mexico to Argentina and the southern Lesser Antilles. Despite recent advances, affinities among typhlopines remain poorly explored, and the phylogenetic relationships and morphology of the South American (SA) species were never accessed before. Here, we performed a phylogenetic analysis including 106 species of Typhlopidae and ten genes. Our dataset represents the most comprehensive for SA species, containing seven of eight recognized species. Corroborating previous studies, we recovered the main groups of Typhlopoidea, and for typhlopines, we recovered with strong support two clades: (a) the Greater Antilles radiation, and the (b) Lesser Antilles and SA radiation. Within the SA radiation, we recovered four main lineages: (a) a clade formed by A. tasymicris and A. minuisquamus; (b) a clade composed by A. reticulatus as the sister group of all other SA species; (c) a clade composed by A. brongersmianus as the sister group of a clade comprising all Northeast Brazilian Species (NBS); and (d) a clade of the NBS, including A. yonenagae, A. arenensis, A. paucisquamus, and A. amoipira. We supplemented our phylogenetic result with the description of hemipenial morphology for seven SA species and comment their relevance to the systematics of Typhlopinae. Hemipenes of SA Amerotyphlops follow the general pattern in scolecophidians (single organ with undivided sulcus). Only A. reticulatus and A. minuisquamus have organs with calcified spines. According to our results, hemipenial ornamentation have shown highly informative and could represent a potential source of systematic and taxonomic characters in that group. We also present an extensive review of the geographical distribution for all SA species. Our study represents the first integrative analysis of a poorly known evolutionary radiation of one of the most widespread SA fossorial snakes.
TL;DR: Molecular data suggest that the potential speciation event occurred around 19–29 Ma, linked with a migration from freshwater to seawater ponds along the Pacific Ocean, and place the flightless marine skater in the genus Dicrotendipes.
Abstract: Insects have invaded marine habitats only rarely and secondarily. Recently, we discovered a flightless dipteran species skating rapidly on the surface of seawater ponds at the Pacific coast of eastern China. Morphological analyses initially suggested an isolated position of the non‐biting midge, suggesting the erection of a new genus within Chironomini (Diptera: Chironomidae). However, an analysis of molecular data revealed that the marine species is in fact nested within the species‐rich genus Dicrotendipes. The apparent conflict between molecular and morphological data can be easily explained. It is likely that the new species has evolved a series of autapomorphic adaptations. These traits clearly distinguish the taxon from other species of the genus but do not justify the erection of a new supraspecific taxon, which would render Dicrotendipes paraphyletic. The switch to marine environments was likely a trigger for various morphological modifications resulting from increased selective pressure. Molecular data suggest that the potential speciation event occurred around 19–29 Ma, linked with a migration from freshwater to seawater ponds along the Pacific Ocean. Considering the results of our analysis, we place the flightless marine skater in the genus Dicrotendipes. All life stages of Dicrotendipes sinicus Qi & Lin sp. n. are described and illustrated, associated with larvae obtained by rearing or confirmed through association with DNA barcodes. The biology and ecology of the species are outlined based on collection data and in situ observations. Evolutionary patterns linked with repeated invasions of marine habitats are discussed.