Independent Evolutionary Lineages Research Articles

Identification and characterization of a new species of Taxus — Taxus qinlingensis by multiple taxonomic methods

BackgroundThe taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.ResultsMultiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500 m.ConclusionsFour characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen & X. T. Wu, sp. nov.

Rediscovery of Lycodongammiei (Blanford, 1878) (Serpentes, Colubridae) in Xizang, China, with comments on its systematic position.

Lycodongammiei (Blanford, 1878), a rarely encountered species of Asian snake, is characterized by ambiguous systematics and biology. Based on a sole specimen of L.gammiei rediscovered in southeastern Xizang, China, we conduct a detailed morphological examination and description, and investigate the systematic position of this species. Morphologically, the newly collected specimen is closely aligned with specimens previously described. Mitochondrial DNA-based phylogenetic analyses reveal that L.gammiei constitutes an independent evolutionary lineage, forming a clade with L.fasciatus (Anderson, 1879), L.gongshan Vogel & Luo, 2011, L.butleri Boulenger, 1900, and L.cavernicolus Grismer, Quah, Anuar, Muin, Wood & Nor, 2014. The closest genetic distance between L.gammiei and its congeners was 10.2%. The discovery of L.gammiei in Medog County, China, signifies an eastward expansion of its known geographical distribution.

Surfing in the Eastern Atlantic: a new bristle millipede from Iberia and the Canary Islands with insights into the phylogeny of Lophoproctus (Diplopoda: Polyxenida: Lophoproctidae)

ABSTRACT The family Lophoproctidae Silvestri, 1897 includes small, blind millipedes adapted to endogeous environments. The genus Lophoproctus has five species with a mostly Mediterranean distribution, with only one species extending eastwards to Central Asia. Lophoproctus lucidus extends from southern France to north-western Africa and was recently reported for the first time from the Iberian Peninsula and the Canary Islands. However, some populations showed a certain degree of morphological differentiation, suggesting the existence of more than one species. To test this hypothesis, we study Iberian and Canarian populations using scanning electron microscopy and analyse mitochondrial and nuclear sequences of several Lophoproctus species, generating the first phylogenetic hypothesis for the genus. Our results confirm the existence of an unnamed species that is here formally described and named as Lophoproctus viator sp. n. The new species can be differentiated morphologically from the other species of the genus and represents an independent evolutionary lineage. We include a key to the morphological identification of Lophoproctus species. http://www.zoobank.org/urn:lsid:zoobank.org:pub:1FFC97EF-279D-4971-B319-E27294CC6D7C

Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum.

The impact of host diversity on the genotypic and phenotypic evolution of broad-spectrum pathogens is an open issue. Here, we used populations of the plant pathogen Ralstonia pseudosolanacearum that were experimentally evolved on five types of host plants, either belonging to different botanical families or differing in their susceptibility or resistance to the pathogen. We investigated whether changes in transcriptomic profiles, associated with or independent of genetic changes, could occur during the process of host adaptation, and whether transcriptomic reprogramming was dependent on host type. Genomic and transcriptomic variations were established for 31 evolved clones that showed better fitness in their experimental host than the ancestral clone. Few genomic polymorphisms were detected in these clones, but significant transcriptomic variations were observed, with a large number of differentially expressed genes (DEGs). In a very clear way, a group of genes belonging to the network of regulation of the bacterial virulence such as efpR, efpH or hrpB, among others, were deregulated in several independent evolutionary lineages and appeared to play a key role in the transcriptomic rewiring observed in evolved clones. A double hierarchical clustering based on the 400 top DEGs for each clone revealed 2 major patterns of gene deregulation that depend on host genotype, but not on host susceptibility or resistance to the pathogen. This work therefore highlights the existence of two major evolutionary paths that result in a significant reorganization of gene expression during adaptive evolution and underscore clusters of co-regulated genes associated with bacterial adaptation on different host lines.

Balitora anlongensis, the first cavefish species of the genus Balitora (Teleostei, Balitoridae) from Guizhou Province, southwest China

This work describes a new species, Balitora anlongensissp. nov., collected from a cave at Xinglong Town, Anlong County, Guzihou, China. Phylogenetic trees reconstructed based on two mitochondrial and three nuclear genes show that the new species represents an independent evolutionary lineage with large genetic differences, 7.1%–12.0% in mitochondrial gene cytochrome b and 9.2%–12.1% in cytochrome oxidase subunit 1, from congeners. Morphologically, the new species can be distinguished from the 18 species currently assigned to the genus Balitora by a combination of characters, most clearly by having two pairs of maxillary barbels; 8½ branched dorsal-fin rays; 5½ branched anal-fin rays; pectoral fin not reaching pelvic fin origin; dorsal-fin origin in front of pelvic fin origin; eye small (eye diameter approximately equal to outer maxillary barbel length); and fins lacking pigment in live fish. The new species represents the first record of Balitora inhabiting caves in China and increases the number of species in the genus Balitora in its present concept from 18 to 19. The study suggests that more evidence is needed to further clarify the taxonomic composition of the genus Balitora.

Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians.

The genetic basis underlying adaptive physiological mechanisms has been extensively explored in mammals after colonizing the seas. However, independent lineages of aquatic mammals exhibit complex patterns of secondary colonization in freshwater environments. This change in habitat represents new osmotic challenges, and additional changes in key systems, such as the osmoregulatory system, are expected. Here, we studied the selective regime on coding and regulatory regions of 20 genes related to the osmoregulation system in strict aquatic mammals from independent evolutionary lineages, cetaceans, and sirenians, with representatives in marine and freshwater aquatic environments. We identified positive selection signals in genes encoding the protein vasopressin (AVP) in mammalian lineages with secondary colonization in the fluvial environment and in aquaporins for lineages inhabiting the marine and fluvial environments. A greater number of sites with positive selection signals were found for the dolphin species compared to the Amazonian manatee. Only the AQP5 and AVP genes showed selection signals in more than one independent lineage of these mammals. Furthermore, the vasopressin gene tree indicates greater similarity in river dolphin sequences despite the independence of their lineages based on the species tree. Patterns of distribution and enrichment of Transcription Factors in the promoter regions of target genes were analyzed and appear to be phylogenetically conserved among sister species. We found accelerated evolution signs in genes ACE, AQP1, AQP5, AQP7, AVP, NPP4, and NPR1 for the fluvial mammals. Together, these results allow a greater understanding of the molecular bases of the evolution of genes responsible for osmotic control in aquatic mammals.

Oreonectesdamingshanensis (Cypriniformes, Nemacheilidae), a new species of stream fish from Guangxi, Southwest China.

In this work, a new species of the genus Oreonectes is described, named Oreonectesdamingshanensis Yu, Luo, Lan, Xiao & Zhou, sp. nov., collected from the Damingshan Mountains of the Guangxi Zhuang Autonomous Region, China. Phylogenetic trees constructed based on the mitochondrial Cyt b showed that the new species represents an independent evolutionary lineage, with uncorrected genetic distances (p-distance) from congeners ranging from 6.1% to 8.9%. Morphologically, the new species can be distinguished from five other species of the genus by a combination of characters. The discovery of this new species raises the number of known species of Oreonectes from five to six. Our study suggests that O.platycephalus may be a complex containing multiple species and that previously recorded areas need to be further delimited and reevaluated.

Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex

Accurate species delimitation is the key to biodiversity conservation and is fundamental to most branches of biology. However, species delimitation remains challenging in those evolutionary radiations associated with mating system transition from outcrossing to self-fertilization, which have frequently occurred in angiosperms and are usually accompanied by rapid speciation. Here, using the Primula cicutariifolia complex as a case, we integrated molecular, morphological and reproductive isolation evidence to test and verify whether its outcrossing (distylous) and selfing (homostylous) populations have developed into independent evolutionary lineages. Phylogenetic trees based on whole plastomes and SNPs of the nuclear genome both indicated that the distylous and homostylous populations grouped into two different clades. Multispecies coalescent, gene flow and genetic structure analyses all supported such two clades as two different genetic entities. In morphology, as expected changes in selfing syndrome, homostylous populations have significantly fewer umbel layers and smaller flower and leaf sizes compared to distylous populations, and the variation range of some floral traits, such as corolla diameter and umbel layers, show obvious discontinuity. Furthermore, hand-pollinated hybridization between the two clades produced almost no seeds, indicating that well post-pollination reproductive isolation has been established between them. Therefore, the distylous and homostylous populations in this studied complex are two independent evolutionary lineages, and thus these distylous populations should be treated as a distinct species, here named Primula qiandaoensis W. Zhang & J.W. Shao sp. nov.. Our empirical study of the P. cicutariifolia complex highlights the importance of applying multiple lines of evidence, in particular genomic data, to delimit species in pervasive evolutionary plant radiations associated with mating system transition.

Complete genome sequence of a new virus from Allium sativum L in China

The complete genome of a new virus belonging to the family Betaflexiviridae was identified in garlic and sequenced by next-generation sequencing and reverse transcription PCR. The complete RNA genome (GenBank accession number OP021693) is 8191 nucleotides in length, excluding the 3' poly(A) tail, and contains five open reading frames (ORFs). These open reading frames encode the viral replicase, triple gene block, and coat protein, and the genome organization is typical of members of the subfamily Quinvirinae. The virus has been tentatively named "garlic yellow curl virus" (GYCV). Phylogenetic analysis suggested that it represents an independent evolutionary lineage in the subfamily, clustering with the currently unclassified garlic yellow mosaic associated virus (GYMaV) and peony betaflexivirus 1 (PeV1). Differences between the phylogenies inferred for the replicase and coat protein indicate that the new virus does not belong to any established genus of the family Betaflexiviridae. This is the first report of GYCV in China.

Systematics and Taxonomy of the Hymenophyllum polyanthos Complex in the Brazilian Atlantic Forest Domain

Abstract— Hymenophyllum subg. Mecodium is subcosmopolitan and comprises ca. 35 species. Its neotropical species are poorly known taxonomically. The high degree of morphological similarity among the species and the absence of clear characters to distinguish them has confounded taxonomic treatments, resulting in the lumping of many putative segregate taxa into a broadly circumscribed Hymenophyllum polyanthos species complex. The goal of the present study was to analyze morphologically and phylogenetically the species of Hymenophyllum subg. Mecodium in the Atlantic Forest domain. Morphological studies were conducted utilizing traditional stereomicroscopy and scanning electron microscopy (SEM). Additionally, Bayesian inference and maximum likelihood phylogenetic analyses were performed using plastid data for seven markers: atpB, atpB-rbcL, matK, rbcL, rbcL-accD, rps4, and rps4-trnS. Seven independent lineages were identified in this study, while morphological analysis supported the delimitation of five taxa within the Atlantic Forest domain: Hymenophyllum apiculatum, H. polyanthos, H. schomburkii, H. undulatum, and H. viridissimum. One taxon, Hymenophyllum sturmii, is recognized as a cryptic species, formed by two independent evolutionary lineages, and treated here provisionally as the H. sturmii complex. A taxonomic revision for the six taxa occurring in the Atlantic Forest domain is presented, including seven new lectotypifications, along with an identification key, descriptions, and illustrations for the species. We also provide data regarding the geographical distribution and conservation status of these six species.

Integrative taxonomy of Imparfinis (Siluriformes, Heptapteridae) from the Upper Paraná River basin, Brazil, with description of a new species

The Neotropical family Heptapteridae comprises 228 valid species widely distributed in South America. Imparfinis is one of the most diverse genera of this family, with 25 valid species widely distributed, inhabiting streams from Costa Rica to Argentina. Old descriptions coupled with lack of recent systematic studies of the species of Imparfinis from the Upper Paraná river basin have led to a taxonomic impediment and hindered the advancement of studies in other areas, such as ecology, cytogenetic, phylogenetic, and evolution. We conducted the first integrative study analyzing both molecular and morphological data of Imparfinis from the Upper Paraná River basin. Our analyses strongly support the existence of four independent evolutionary lineages in this river system, three of them are the nominal species I. mirini, I. schubarti, and I. piperatus, and a new species from Goiás state described herein.

Transposable elements maintain genome-wide heterozygosity in inbred populations

Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding. Capitalizing on the mixed mating system of Arabidopsis lyrata, we assess genome-wide heterozygosity and signatures of selection at single nucleotide polymorphisms near transposable elements across an inbreeding gradient. Under intense inbreeding, we find systematically elevated heterozygosity downstream of several TE superfamilies, associated with signatures of balancing selection. In addition, we demonstrate increased heterozygosity in stress-responsive genes that consistently occur downstream of TEs. We finally reveal that TE superfamilies are associated with specific signatures of selection that are reproducible across independent evolutionary lineages of A. lyrata. Together, our study provides an important hypothesis for the success of self-fertilizing species.

Update: Assessing the evolutionary trajectory of the Apaporis caiman (Caiman crocodilus apaporiensis, Medem 1955) via mitochondrial molecular markers

Abstract The spectacled caiman (Caiman crocodilus) is currently considered to be a species complex due to the relatively high morphological and molecular diversity expressed across its range. One of the populations of interest, inhabiting the Apaporis River (Colombia), was described based on skull features as an incipient species (C. c. apaporiensis) and has been treated by some authors as a full species. Recent molecular work challenged this hypothesis, because relatively low mitochondrial molecular differentiation was found between the morphologically described Apaporis caiman and C. crocodilus (s.s.) Amazonian populations. Here, we present an update on the topic based on a larger molecular sample size and on analysis of expanded geometric morphometric data that include six newly collected skulls. Morphometric data support the existence of previously recognized morphotypes within the complex in Colombia and demonstrate that the newly collected material can be assigned to the classic Apaporis caiman morphotype. However, our expanded genetic analysis fails to find appreciable mitochondrial molecular divergence of the Apaporis caiman population from the C. c. crocodilus population (COI-CytB: Amazon Peru 0.17 ± 0.06%, CytB-only: Caquetá River Colombia 0.08 ± 0.07%). The Apaporis caiman is interpreted to be a phenotypically distinct member of the cis-Andean C. crocodilus metapopulation that has not yet achieved (or may not be undergoing at all) appreciable genetic differentiation. Thus, it should not be considered a fully independent evolutionary lineage, nor given full species rank.

Phylogenomic analysis of the bowfin (Amia calva) reveals unrecognized species diversity in a living fossil lineage

The Bowfin (Amia calva), as currently recognized, represents the sole living member of the family Amiidae, which dates back to approximately 150 Ma. Prior to 1896, 13 species of extant Bowfins had been described, but these were all placed into a single species with no rationale or analysis given. This situation has persisted until the present day, with little attention given to re-evaluation of those previously described nominal forms. Here, we present a phylogenomic analysis based on over 21,000 single nucleotide polymorphisms (SNPs) from 94 individuals that unambiguously demonstrates the presence of at least two independent evolutionary lineages within extant Amia populations that merit species-level standing, as well as the possibility of two more. These findings not only expand the recognizable species diversity in an iconic, ancient lineage, but also demonstrate the utility of such methods in addressing previously intractable questions of molecular systematics and phylogeography in slowly evolving groups of ancient fishes.

Aneuploidy promotes intraspecific diversification of the endemic East Asian herb Lycoris aurea complex.

Polyploidy has received considerable interest in the past, but aneuploidy and partial rearrangements may also influence genomic divergence. In this study, we reported a comprehensive cytogeographic, morphological and genetic analysis of Lycoris aurea complex throughout its range and attempted to explore the association between aneuploidy and species diversification. The karyotypes of this complex presented aneuploidy variations mainly divided into four cytotypes: I (2n = 10m + 2T), II (2n = 8m + 6T), III (2n = 7m + 8T), and IV (2n = 6m + 10T). Cytotype distributions were highly structured geographically. Two main cytotypes, II and IV, are geographically allopatric. The populations with cytotype II are mainly distributed in central China and the southern islands of Japan. Cytotypes IV is disjunctly distributed in southwestern and southeastern China. The cytotypes with fewer chromosome numbers tend to occur at high latitudes. For analyzing the phylogeographic pattern and genetic structure of this complex, we sequenced four chloroplast DNA fragments (4,748 bp in total) of 241 individuals from 42 populations. Extremely high diversity of cpDNA haplotypes was found, with genetic diversity index (Hd) being 0.932 and 98.61% of the genetic variation occurring among populations, indicating that this complex has undergone strong intraspecific differentiation. The cytotype II had the highest haplotype diversity (Hd = 0.885), while cytotype IV harbored the highest nucleotide diversity (π = 4.09 × 10–3). We detected significant leaf morphological differences not only between cytotype II and IV but also between west lineage and east lineage within cytotype IV. These results illustrated that aneuploidy contributed to extensive morphological and genetic differentiation in L. aurea complex. It was suggested that L. aurea complex should comprise multiple independent evolutionary lineages, and accurate species delimitation needs to be established further in an integrative taxonomic approach.

The colonisation of saline waters is associated with lowered immune responses in aquatic beetles

Abstract The immune response represents a suite of evolved traits that can involve energetic and evolutionary trade‐offs with other energy‐demanding and fitness‐related processes. Here, we tested the hypothesis that aquatic beetles living in inland hypersaline habitats have lower immune capacity than freshwater congeners. Phenoloxidase activity, encapsulation response and antimicrobial peptide activity were compared in freshwater/hypersaline species pairs with differing osmoregulatory capacity and cuticular waterproofing properties in the genera Nebrioporus (Dytiscidae) and Enochrus (Hydrophilidae), independent evolutionary lineages that have colonised saline media separately. Hypersaline species (N. ceresyi and E. jesusarribasi) showed significantly lower phenoloxidase activity and antimicrobial peptide responses than their freshwater relatives (N. clarkii and E. salomonis). Encapsulation responses in freshwater species also appeared to be higher than in hypersaline relatives. Our results reinforce the complex nature of immune responses and suggest that adaptation to saline environments may have involved a trade‐off between osmoregulation and investment in immune defences, but also are consistent with relaxed selection pressures on basal immune responses resulting from lower microbial infection load in saline habitats. In addition, the more resistant cuticle of species occupying such habitats may protect against the entry of parasites, reducing selection pressure on immunity. Because the evolution of salinity tolerance is associated with reduced immune capacity, saline specialists may be particularly vulnerable to the dilution of saline waters and consequent changes in pathogen communities and load following colonisation by more generalist microorganisms.

Multilocus Data Analysis Reveal the Diversity of Cryptic Species in the Tillandsia ionantha (Bromeliaceae: Tillansiodeae) Complex.

Independent evolutionary lineages or species that lack phenotypic variation as an operative criterion for their delimitation are known as cryptic species. However, these have been delimited using other data sources and analysis. The aims of this study are: (1) to evaluate the divergence of the populations of the T. ionantha complex; and (2) to delimit the species using multilocus data, phylogenetic analysis and the coalescent model. Phylogenetic analyses, genetic diversity and population structure, and isolation by distance analysis were performed. A multispecies coalescent analysis to delimit the species was conducted. Phylogenetic analysis showed that T. ionantha is polyphyletic composed of eight evolutionary lineages. Haplotype distribution and genetic differentiation analysis detected strong population structure and high values of genetic differentiation among populations. The positive correlation between genetic differences with geographic distance indicate that the populations are evolving under the model of isolation by distance. The coalescent multispecies analysis performed with starBEAST supports the recognition of eight lineages as different species. Only three out of the eight species have morphological characters good enough to recognize them as different species, while five of them are cryptic species. Tillandsia scaposa and T. vanhyningii are corroborated as independent lineages, and T. ionantha var. stricta changed status to the species level.

Catalogue of primary types of Neotropical Myotis (Chiroptera, Vespertilionidae).

Myotis comprises a diverse group of vespertilionid bats with worldwide distribution. Neotropical Myotis have an accentuated phenotypic conservatism, which makes species delimitation and identification difficult, hindering our understanding of the diversity, distribution, and phylogenetic relationships of taxa. To encourage new systematic reviews of the genus, a catalogue of the primary types and names is presented, current and in synonymy, for Neotropical Myotis. Currently 33 valid species (and three subspecies) are recognized, and their primary types are deposited in 12 scientific collections in the USA (30 types), Brazil (two types), England (two types), and France (one type). The names of 29 Neotropical Myotis species currently in synonymy were found. However, it is possible that some synonyms represent independent evolutionary lineages, considering recent results provided by taxonomic revisions.

An updated checklist of the herpetofauna from Isla María Cleofas, Mexico

We provide an updated checklist of amphibians and reptiles from Isla María Cleofas, Mexico. This island is located at the Islas Marías Archipelago Biosphere Reserve on the coast of the state of Nayarit. The herpetofaunal diversity of Isla María Cleofas has been addressed for over a century; however, the literature is limited just a few scientific explorations and occasional records. In addition, previous herpetofaunal lists contain taxonomic inaccuracies, which are revised here, and recent nomenclatural changes are incorporated. Records of three newly reported species, Lampropeltis polyzona Cope, 1860, Leptophis diplotropis (Günther, 1872) and Tantilla calamarina Cope, 1866, were obtained during our fieldwork. Based on both our field observations and a literature review, the herpetofauna of Isla María Cleofas includes 16 species (two amphibians and 14 reptiles). We also review the conservation status of all species using three independent systems [NOM 059-SEMARNAT-2010, IUCN, and environmental vulnerability score (EVS)]. Finally, we discuss the likely occurrence of evolutionary independent lineages on the island.

Molecular markers and SEM imaging reveal pseudocryptic diversity within the Ponto-Caspian low-profile amphipod invader Dikerogammarus bispinosus

The Ponto-Caspian amphipod Dikerogammarus bispinosus was originally described from the Black Sea basin. Its recent discovery in the Caspian Sea basin was puzzling because it was unknown whether it was an invasive or an overlooked native species in this area. Here, we examined specimens collected from both the Black and Caspian Sea basins by means of molecular species delimitation based on nuclear (28S) and mitochondrial (COI) DNA sequences, as well as scanning electron microscopy (SEM). Our analyses reveal that D. bispinosus comprises three evolutionary independent lineages that are molecularly and morphologically distinct. One lineage occurs throughout rivers in the Black Sea basin, while the other two inhabit the Caspian Sea and were found in sympatry, further reinforcing that they are distinct species. Our time-calibrated phylogeny indicates that these lineages split during the Late Miocene-Pliocene, a period corresponding with the separation of the Black and Caspian basins via the Caucasus mountain uplift. SEM imaging revealed morphological differences with respect to setal patterns on the gnathopod propodi among all three lineages. Therefore, our results clearly indicate not only that D. bispinosus is native in the Caspian region, but that it has been overlooked for a long time. Additional populations covering the entire range of this species complex need to be further studied in order to gain a more complete picture of its evolutionary history and resolve its taxonomy.