Distinct Evolutionary Lineages Research Articles

Genetic Divergence of Philippine Tarsiers, Based on the 12S rRNA Gene, and its Implication for Their Taxonomic and Conservation Status

The recent identification of distinct Philippine tarsier evolutionary lineages has raised concern over both the taxonomy and conservation status of the species across its geographical range. Its listing among the world’s most endangered primates from 2014–2016 further emphasized the need to address the previously unresolved issues regarding its taxonomy. However, the information needed for proper taxonomic resolution is still lacking. In this study, the genetic distances among the Philippine tarsier evolutionary lineages based on the mitochondrial 12S rRNA gene were estimated and compared with those of Eastern tarsier species from Sulawesi in order to build on the existing genetic information about them. Maximum likelihood (ML) analyses and Bayesian inference (BI) were used to infer phylogenetic trees from which groupings were recovered. Phylogenetic relationships were supplemented by a median-joining haplotype network analysis. Monophyletic tarsier clades were supported by the inferred trees. Groups corresponding to evolutionary lineages and species identified in the respective reference literature were recovered within both the Philippine tarsier and the Eastern tarsier clades. Among the Philippine tarsier groups, only the Dinagat-Caraga group was both strongly supported and monophyletic, whereas other groups exhibited a mixture of some samples among various haplotype clades. Pairwise genetic GTR+G distances among the Philippine tarsier groups ranged from 0.76–1.31%, and were found to be within the range or even higher than some of the genetic distances among Eastern tarsier species that ranged from 0.67–3.96%. Patterns among pairwise genetic distances suggest possible species-level distinction among the Philippine tarsier groups, with particular emphasis on the Dinagat-Caraga group and a possibility of crypsis within the Mindanao group, although further taxonomic input following an integrative approach is still needed. Recommendations for the priority research steps that are geared toward resolving taxonomic iss

The unusual biology of marine file snakes with a perspective for the conservation of Acrochordus granulatus

Biodiversity and the function of tropical shallow-water marine environments are threatened by numerous anthropogenic factors, especially climate change, overharvesting of resources, and destruction of habitat. Marine snakes are important components of coastal shallow-water systems and should be considered as indicators of the health of coastal ecosystems such as mangroves. Acrochordid snakes (Acrochordidae: Acrochordus) represent a highly distinct evolutionary lineage with unusual adaptations to shallow water habitats and importance to biodiversity of tropical coastal regions. One of three congeneric species, Acrochordus granulatus (file snake), is an interesting and common inhabitant of coastal estuaries and mangroves in the Philippines. This paper reviews unusual attributes of A. granulatus and provides a perspective for its conservation in coastal habitats. Morphological, physiological, and behavioral characters of this snake are specialized for life in shallow-water marine environments such as mangroves. Unusual and specialized features confer abilities for prolonged submergence and include low metabolic rate, large capacity for oxygen storage, cutaneous gas exchange, nearly complete utilization of oxygen stores during aerobic submergence, intracardiac and cutaneous shunts for regulating blood flow, and reclusive behavior. Fresh water is required for water balance, and file snakes are dependent on rainfall in many habitats where they drink from freshwater lenses formed by precipitation on the surfaces of marine water. File snakes feed largely on fishes and are candidates as bio-indicators of the health of shallow-water coastal habitats. Attention should be given to threatening insults on coastal environments including climate change, habitat destruction, harvesting of resources, and other factors in need of research, monitoring, and plans for abatement. Importantly, conservation can be promoted by educating people about the docile behavior, unusual traits, and interesting ecology of A. granulatus. KEYWORDS: mangrove, shallow water, Acrochordidae, little file snake, conservation physiology, ecophysiology

Molecular phylogeny and character evolution of Flemingia (Leguminosae, Papilionoideae, Phaseoleae, Cajaninae) inferred from three cpDNA and nrITS sequence data

The genus Flemingia belonging to the family Leguminosae (Papilionoideae, Phaseoleae, Cajaninae) comprises ca. 30–35 species and is distributed mainly in tropical and subtropical Africa, Asia and Oceania. Previous systematic studies of the genus Flemingia were based on morphology only, or aimed at reconstructing relationships, delimiting distinct evolutionary lineages based on morphological and molecular data, focusing on its allied genera or the tribe Phaseoleae as a whole and thus included a limited sampling of the genus Flemingia. In this present study, phylogeny of Flemingia was inferred from molecular data of three cpDNA plastid markers (matK, rps16-trnQ, and psbA-trnH) and one nuclear region (nrITS) of 73 accessions representing ca. 31 species and all five previously recognized infrageneric groups (subgenus/section) of Flemingia. Results revealed the para- and polyphyly of four previously recognized subgenera/sections within the genus Flemingia, the exception for the group Lepidocoma. Our nuclear phylogeny recovered four major clades and one single species clade, F. faginea. This species was, however, grouped in clade III (Ostryodium group) in chloroplast phylogeny. Incongruence between the trees of chloroplast and nuclear markers may point to either introgression or incomplete lineage sorting. Furthermore, the evolution of three major morphological features in Flemingia was discussed. The results of this research are not in the favor of synonymization of F. glutinosa with F. lineata, and F. ferruginea, F. cumingiana, F. phillipinensis, F. latifolia, F. prostrata, F. stricta, F. wallichi, F. grahamiana, F. sootepensis with F. macrophylla.

Youngest jalodontid shark from the Triassic of Europe and a revision of the Jalodontidae

ABSTRACT Phoebodont-like teeth originally described as Phoebodus brodiei and Phoebodus keuperinus from the Upper Triassic of England and Germany, respectively, are attributed to a new genus Keuperodus of the family Jalodontidae. The characteristic features of all jalodontid genera are re-examined leading to the conclusion that this group formed a separate, distinct chondrichthyan evolutionary line for which a new order, the Jalodontiformes is established. The jalodontid dentition evolved from a homodont-like type to one which was markedly heterodont.

Nonparallel transcriptional divergence during parallel adaptation.

How underlying mechanisms bias evolution toward predictable outcomes remains an area of active debate. In this study, we leveraged phenotypic plasticity and parallel adaptation across independent lineages of Trinidadian guppies (Poecilia reticulata) to assess the predictability of gene expression evolution during parallel adaptation. Trinidadian guppies have repeatedly and independently adapted to high- and low-predation environments in the wild. We combined this natural experiment with a laboratory breeding design to attribute transcriptional variation to the genetic influences of population of origin and developmental plasticity in response to rearing with or without predators. We observed substantial gene expression plasticity, as well as the evolution of expression plasticity itself, across populations. Genes exhibiting expression plasticity within populations were more likely to also differ in expression between populations, with the direction of population differences more likely to be opposite those of plasticity. While we found more overlap than expected by chance in genes differentially expressed between high- and low-predation populations from distinct evolutionary lineages, the majority of differentially expressed genes were not shared between lineages. Our data suggest alternative transcriptional configurations associated with shared phenotypes, highlighting a role for transcriptional flexibility in the parallel phenotypic evolution of a species known for rapid adaptation.

Phylogeny and Strain Typing of Wolbachia from Yamatotettix flavovittatus Matsumura Leafhoppers.

Wolbachia is a maternally inherited bacterium of insects that can alter the reproduction, biology, and fitness of the hosts. It was detected in natural populations of the Yamatotettix flavovittatus Matsumura leafhoppers, the vector of phytoplasma, which is responsible for sugarcane white leaf disease. Wolbachia infection prolongs the longevity of female leafhoppers and promotes a strong reproductive incompatibility; importantly, highly maternal transmission rate was observed. However, limited data on the diversity or strain typing of Wolbachia in Y. flavovittatus are available. We aimed here to detect the presence of Wolbachia in different populations by amplification of the wsp gene, which was then sequenced. Multilocus sequence typing (MLST) was also performed to explore the diversity of the Wolbachia strains. Based on the wsp sequences, Wolbachia in the Y. flavovittatus leafhoppers belonged to supergroup B, and formed a distinct evolutionary lineage; therefore, we designated this new specific strain as wYfla. The MLST profiles revealed ten potential new sequence types (STs) in different leafhopper populations. Multiple STs were detected in individual leafhoppers, among which the ST-wYfla1 strain was predominant. Furthermore, we obtained congruent results for the phylogenetic analyses using the wsp gene and MLST loci. To the best of our knowledge, this is the first study characterizing Wolbachia strains in Y. flavovittatus. Our results reveal a novel strain and multiple STs of Wolbachia, and these data may prove useful in the exploitation of Wolbachia as a biological Y. flavovittatus control agent.

Completing a taxonomic puzzle: integrative review of geckos of the Paroedura bastardi species complex (Squamata, Gekkonidae)

The Paroedura bastardi clade, a subgroup of the Madagascan gecko genus Paroedura, currently comprises four nominal species: P. bastardi, supposedly widely distributed in southern and western Madagascar, P. ibityensis, a montane endemic, and P. tanjaka and P. neglecta, both restricted to the central west region of the island. Previous work has shown that Paroedura bastardi is a species complex with several strongly divergent mitochondrial lineages. Based on one mitochondrial and two nuclear markers, plus detailed morphological data, we undertake an integrative revision of this species complex. Using a representative sampling for seven nuclear and five mitochondrial genes we furthermore propose a phylogenetic hypothesis of relationships among the species in this clade. Our analyses reveal at least three distinct and independent evolutionary lineages currently referred to P. bastardi. Conclusive evidence for the species status of these lineages comes from multiple cases of syntopic occurrence without genetic admixture or morphological intermediates, suggesting reproductive isolation. We discuss the relevance of this line of evidence and the conditions under which concordant differentiation in unlinked loci under sympatry provides a powerful approach to species delimitation, and taxonomically implement our findings by (1) designating a lectotype for Paroedura bastardi, now restricted to the extreme South-East of Madagascar, (2) resurrecting of the binomen Paroedura guibeae Dixon & Kroll, 1974, which is applied to the species predominantly distributed in the South-West, and (3) describing a third species, Paroedura rennerae sp. nov., which has the northernmost distribution within the species complex.

Completing a taxonomic puzzle: integrative review of geckos of the Paroedura bastardi species complex (Squamata, Gekkonidae)

The Paroedura bastardi clade, a subgroup of the Madagascan gecko genus Paroedura, currently comprises four nominal species: P. bastardi, supposedly widely distributed in southern and western Madagascar, P. ibityensis, a montane endemic, and P. tanjaka and P. neglecta, both restricted to the central west region of the island. Previous work has shown that Paroedura bastardi is a species complex with several strongly divergent mitochondrial lineages. Based on one mitochondrial and two nuclear markers, plus detailed morphological data, we undertake an integrative revision of this species complex. Using a representative sampling for seven nuclear and five mitochondrial genes we furthermore propose a phylogenetic hypothesis of relationships among the species in this clade. Our analyses reveal at least three distinct and independent evolutionary lineages currently referred to P. bastardi. Conclusive evidence for the species status of these lineages comes from multiple cases of syntopic occurrence without genetic admixture or morphological intermediates, suggesting reproductive isolation. We discuss the relevance of this line of evidence and the conditions under which concordant differentiation in unlinked loci under sympatry provides a powerful approach to species delimitation, and taxonomically implement our findings by (1) designating a lectotype for Paroedura bastardi, now restricted to the extreme South-East of Madagascar, (2) resurrecting of the binomen Paroedura guibeae Dixon & Kroll, 1974, which is applied to the species predominantly distributed in the South-West, and (3) describing a third species, Paroedura rennerae sp. nov., which has the northernmost distribution within the species complex.

Criibacterium bergeronii gen. nov., sp. nov., a new member of the family Peptostreptococcaceae, isolated from human clinical samples.

A rod-shaped, motile anaerobic bacterium, designated CCRI-22567T, was isolated from a vaginal sample of a woman diagnosed with bacterial vaginosis and subjected to a polyphasic taxonomic study. The novel strain was capable of growth at 30–42 °C (optimum, 42 °C), at pH 5.5–8.5 (optimum, pH 7.0–7.5) and in the presence of 0–1.5 % (w/v) NaCl (optimally at 0.5 % NaCl). The phylogenetic trees based on 16S rRNA gene sequences showed that strain CCRI-22567T forms a distinct evolutionary lineage independent of other taxa in the family Peptostreptococcaceae. Strain CCRI-22567T exhibited 90.1 % 16S rRNA gene sequence similarity to Peptoanaerobacter stomatis ACC19aT and 89.7 % to Eubacterium yurii subsp. schtitka ATCC 43716. The three closest organisms with an available whole genome were compared to strain CCRI-22567T for genomic relatedness assessment. The genomic average nucleotide identities (OrthoANIu) obtained with Peptoanaerobacter stomatis ACC19aT, Eubacterium yurii subsp. margaretiae ATCC 43715 and Filifactor alocis ATCC 35896T were 71.8, 70.3 and 69.6 %, respectively. Strain CCRI-22567T contained C18 : 1 ω9c and C18 : 1 ω9c DMA as the major fatty acids. The DNA G+C content of strain CCRI-22567T based on its genome sequence was 33.8 mol%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain CCRI-22567T is considered to represent a new genus and species within the family Peptostreptococcaceae, for which the name Criibacterium bergeronii gen. nov., sp. nov., is proposed. The type strain of Criibacterium bergeronii is CCRI-22567T (=LMG 31278T=DSM 107614T=CCUG 72594T).

Phylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability.

Salmonella enterica subspecies arizonae is frequently associated with animal reservoirs, particularly reptiles, and can cause illness in some mammals, including humans. Using whole-genome sequencing data, core genome phylogenetic analyses were performed using 112 S . enterica subsp. arizonae isolates, representing 46 of 102 described serovars. Nearly one-third of these are polyphyletic, including two serovars that appear in four and five distinct evolutionary lineages. Subspecies arizonae has a monophasic H antigen. Among the 46 serovars investigated, only 8 phase 1 H antigens were identified, demonstrating high conservation for this antigen. Prophages and plasmids were found throughout this subspecies, including five novel prophages. Polyphyly was also reflected in prophage content, although some clade-specific enrichment for some phages was observed. IncFII(S) was the most frequent plasmid replicon identified and was found in a quarter of S. enterica subsp. arizonae genomes. Salmonella pathogenicity islands (SPIs) 1 and 2 are present across all Salmonella , including this subspecies, although effectors sipA, sptP and arvA in SPI-1 and sseG and ssaI in SPI-2 appear to be lost in this lineage. SPI-20, encoding a type VI secretion system, is exclusive to this subspecies and is well maintained in all genomes sampled. A number of fimbral operons were identified, including the sas operon that appears to be a synapomorphy for this subspecies, while others exhibited more clade-specific patterns. This work reveals evolutionary patterns in S. enterica subsp. arizonae that make this subspecies a unique lineage within this very diverse species.

Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia

BackgroundAs the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens.ResultsThis study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006–2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations.ConclusionsThese results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia.ADx5T_Q3aYxBw7CRZGTwQ6Video abstract

SNP-Density Crossover Maps of Polymorphic Transposable Elements and HLA Genes Within MHC Class I Haplotype Blocks and Junction.

The genomic region (~4 Mb) of the human major histocompatibility complex (MHC) on chromosome 6p21 is a prime model for the study and understanding of conserved polymorphic sequences (CPSs) and structural diversity of ancestral haplotypes (AHs)/conserved extended haplotypes (CEHs). The aim of this study was to use a set of 95 MHC genomic sequences downloaded from a publicly available BioProject database at NCBI to identify and characterise polymorphic human leukocyte antigen (HLA) class I genes and pseudogenes, MICA and MICB, and retroelement indels as haplotypic lineage markers, and single-nucleotide polymorphism (SNP) crossover loci in DNA sequence alignments of different haplotypes across the Olfactory Receptor (OR) gene region (~1.2 Mb) and the MHC class I region (~1.8 Mb) from the GPX5 to the MICB gene. Our comparative sequence analyses confirmed the identity of 12 haplotypic retroelement markers and revealed that they partitioned the HLA-A/B/C haplotypes into distinct evolutionary lineages. Crossovers between SNP-poor and SNP-rich regions defined the sequence range of haplotype blocks, and many of these crossover junctions occurred within particular transposable elements, lncRNA, OR12D2, MUC21, MUC22, PSORS1A3, HLA-C, HLA-B, and MICA. In a comparison of more than 250 paired sequence alignments, at least 38 SNP-density crossover sites were mapped across various regions from GPX5 to MICB. In a homology comparison of 16 different haplotypes, seven CEH/AH (7.1, 8.1, 18.2, 51.x, 57.1, 62.x, and 62.1) had no detectable SNP-density crossover junctions and were SNP poor across the entire ~2.8 Mb of sequence alignments. Of the analyses between different recombinant haplotypes, more than half of them had SNP crossovers within 10 kb of LTR16B/ERV3-16A3_I, MLT1, Charlie, and/or THE1 sequences and were in close vicinity to structurally polymorphic Alu and SVA insertion sites. These studies demonstrate that (1) SNP-density crossovers are associated with putative ancestral recombination sites that are widely spread across the MHC class I genomic region from at least the telomeric OR12D2 gene to the centromeric MICB gene and (2) the genomic sequences of MHC homozygous cell lines are useful for analysing haplotype blocks, ancestral haplotypic landscapes and markers, CPSs, and SNP-density crossover junctions.

Alkalicaulis satelles gen. nov., sp. nov., a novel haloalkaliphile isolated from a laboratory culture cyanobacterium Geitlerinema species and proposals of Maricaulaceae fam. nov., Robiginitomaculaceae fam. nov., Maricaulales ord. nov. and Hyphomonadales ord. nov.

A prosthecate bacterial strain, designated G-192T, was isolated from decaying biomass of a haloalkaliphilic cyanobacterium Geitlerinema sp. Z-T0701. The cells were aerobic, Gram-negative, non-endospore-forming and dimorphic, occurring either as sessile bacteria with a characteristic stalk or as motile flagellated cells. The strain utilized a limited range of substrates, mostly peptonaceous, but was able to degrade whole proteins. Growth occurred at 5-46 °C (optimum, 35-40 °C), pH 7.3-10.3 (optimum, pH 8.0-9.0), 0-14 % NaCl (v/w; optimum, 2.0-6.0 %, v/w). The G+C content of the genomic DNA of strain G-192T was 66.8%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain G-192T formed a distinct evolutionary lineage within the family Hyphomonadaceae. Strain G-192T showed the highest 16S rRNA sequence similarity to Glycocaulis profundi ZYF765T (95.2%), Oceanicaulis stylophorae GISW-4T (94.2%) and Marinicauda salina WD6-1T (95.5%). The major cellular fatty acids (>5% of the total) were C18:1 ω9c, C18:0 and 11-methyl-C18:1 ω7c. The major polar lipids were glycolipids and phospholipids. The only respiratory quinone was ubiquinone-10 (Q-10). Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain G-192T represents a novel species of a new genus, for which the name Alkalicaulis satelles gen. nov., sp. nov. is proposed. The type strain is G-192T (=VKM B-3306T=KCTC 72746T). The strain is the first representative of the stalked bacteria associated with a haloalkaliphilic cyanobacterium. Based on phylogenomic indices and phenotypic data, it is proposed to evolve two novel families Maricaulaceae fam. nov. and Robiginitomaculaceae fam. nov. out of the current family Hyphomonadaceae. In addition, it is proposed to place the first two families in the novel order Maricaulales ord. nov. and novel order Hyphomonadales ord. nov. is proposed to accommodate the family Hyphomonadaceae.

Resolving the systematics of Richtersiidae by multilocus phylogeny and an integrative redescription of the nominal species for the genus Crenubiotus (Tardigrada)

The family Richtersiidae, although established recently with the use of phylogenetic methods, was considered potentially paraphyletic at the time of its erection. Until now, the family comprised four genera, Richtersius, Diaforobiotus, Adorybiotus and a newly erected genus Crenubiotus. However, the genetic characterisation for the latter two genera was very limited or absent. To address concerns about the phylogenetic affinity of these two genera, we present a multilocus phylogeny of the families Richtersiidae and Murrayidae based on four molecular markers (18S rRNA, 28S rRNA, ITS-2 and COI). Our results show a distinct evolutionary lineage composed of Adorybiotus and Crenubiotus, which is sister to Murrayidae. In order to accommodate the phylogenetic and morphological distinctiveness of this lineage, we erect a new family, Adorybiotidae fam. nov. The new taxon differs morphologically from other families in the superfamily Macrobiotoidea by a unique combination of traits: (1) the presence of tubercles/cushions with aggregations of microgranules on their surfaces present on all legs and on the dorso-caudal cuticle, (2) a system of internal septa in claws, and (3) buccal apparatus morphology. Moreover, in order to stabilise the taxonomy and nomenclature in the genus Crenubiotus, we redescribe its type species, Crenubiotus crenulatus, by means of integrative taxonomy and designate a new neotype based on a population from the original terra typica.

Regional drivers of diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus

AbstractAimPleistocene climate and associated environmental changes have influenced phylogeographic patterns of many species. These not only depend on a species’ life history but also vary regionally. Consequently, populations of widespread species that occur in several biomes might display different evolutionary trajectories. We aimed to identify regional drivers of diversification in the common pheasant, a widely distributed ecological generalist.LocationAsia.TaxonCommon pheasant Phasianus colchicus.MethodsUsing a comprehensive geographical sampling of 204 individuals from the species’ entire range genotyped at seven nuclear and two mitochondrial loci, we reconstructed spatio‐temporal diversification and demographic history of the common pheasant. We applied Bayesian phylogenetic inference to describe phylogeographic structure, generated a species tree and inferred demographic history within and migration between lineages. Moreover, to establish a taxonomic framework, we conducted a species delimitation analysis.ResultsThe common pheasant diversified during the Late Pleistocene into eight distinct lineages. It originated at the edge of the Qinghai–Tibetan plateau and spread to East and Central Asia. Only the widely distributed lowland lineage of East Asia displayed recent range expansion. Greater phylogeographic structure was identified elsewhere, with lineages showing no sign of recent demographic changes. One lineage in south‐central China is the result of long‐term isolation within a climatically stable but topographically complex region. In lineages from arid Central Asia and China, range expansions were impeded by repeated population fragmentation during dry glacial periods and by recent aridification.Main conclusionsSpatio‐temporal phylogeographic frameworks of widespread taxa such as the common pheasant provide valuable opportunities to identify divergent drivers of regional diversification. Our results suggest that diversification and population histories in the eight distinct evolutionary lineages were shaped by regionally variable effects of past climate and associated environmental changes. The evolutionary history of the common pheasant is best reflected by its being split into three species.

Evolutionary Origins of Three Rare Alpine-Endemic Species ofLomatium(Apiaceae) in the Wallowa and Elkhorn Mountains of Northeastern Oregon

Premise of research. Shared ancestry and convergent/parallel evolution are the two primary causes of morphologically similar species occurring in similar climatic niches. Alpine habitats harbor a unique biodiversity that is often characterized by many convergences in life-forms, such as cushion and rosulate habits. Three species of Lomatium (L. greenmanii, L. erythrocarpum, and L. oreganum) are high-alpine specialists endemic to the Wallowa and Elkhorn Mountains of northeastern Oregon. Earlier studies suggested that two of these species might be sister taxa, but because of the prevalence of convergence in alpine habitats and recent studies that have highlighted morphological homoplasy among Lomatium species, this hypothesis warrants reconsideration.Methodology. Phylogenetic analysis of 209 individuals representing 79 taxa belonging to subfamily Apioideae (Apiaceae) was used to investigate the evolutionary origins of three alpine-endemic species of Lomatium. A principal components analysis based on BioClim variables was used to further investigate species climatic niches.Pivotal results. The three alpine-endemic species of Lomatium from northeastern Oregon represent three independent origins of alpine adaptations rather than a single or two alpine radiations, as previously suggested.Conclusions. Convergence and parallelism are especially common in alpine habitats and among Lomatium species, a finding confirmed by this study. This study unveils unpredicted phylogenetic diversity in the Wallowa and Elkhorn Mountains, which, therefore, calls for appropriate conservation measures to protect these distinct evolutionary lineages.

Multiple invasions of a generalist herbivore-Secondary contact between two divergent lineages of Nezara viridula Linnaeus in Australia.

The presence of distinct evolutionary lineages within herbivorous pest insect taxa requires close attention. Scientific understanding, biosecurity planning and practice, and pest management decision‐making each suffer when such situations remain poorly understood. The pest bug Nezara viridula Linnaeus has been recorded from numerous host plants and has two globally distributed mitochondrial (mtDNA) lineages. These mtDNA lineages co‐occur in few locations globally, and the consequences of their divergence and recent secondary contact have not been assessed. We present evidence that both mtDNA lineages of N. viridula are present in Australia and their haplotype groups have a mostly separate distribution from one another. The north‐western population has only Asian mtDNA haplotypes, and the population with an eastern distribution is characterized mostly by European mtDNA haplotypes. Haplotypes of both lineages were detected together at only one site in the north of eastern Australia, and microsatellite data indicate that this secondary contact has resulted in mating across the lineages. Admixture and the movement of mtDNA haplotypes outside of this limited area of overlap has not, however, been extensive. Some degree of mating incompatibility or differences in the climatic requirements and tolerances of the two lineages, and perhaps a combination of these influences, might limit introgression and the movement of individuals, but this needs to be tested. This work provides the foundation for further ecological investigation of the lineages of N. viridula, particularly the consequences of admixture on the ecology of this widespread pest. We propose that for now, the Asian and European lineages of N. viridula would best be investigated as subspecies, so that “pure” and admixed populations of this bug can each be considered directly with respect to management and research priorities.

Taxonomic Revision of Philippine Sun Skinks (Reptilia: Squamata: Scincidae: Eutropis), and Descriptions of Eight New Species

Species descriptions of reptiles historically have relied exclusively on the use of morphological data; however, these external, phenotypic data do not always co-vary with lineage divergence. Consequently, it has become increasingly clear that species diversity has been underestimated in many evolutionary radiations. With the use of an integrative approach, we examined the genetic and morphological diversity present in a nearly endemic Philippine radiation of Eutropis. Results demonstrated that current taxonomy does not reflect evolutionary history and that in many cases, morphological divergence has become decoupled from genetic divergence. As a consequence, species diversity is significantly underestimated. Here, we rectify the major taxonomic problems present in Philippine Eutropis by providing formal descriptions for eight new species. Three of the four new species in the E. multicarinata species complex are sympatric with (and have long been confused with) previously described subspecies (which we also elevate to full species here). The fourth species is endemic to the Caroline Islands, clearly derived from a long-distance dispersal event from the Philippines. The new species in the E. indeprensa species complex are allopatrically or parapatrically distributed across the archipelago. In contrast to the last review of Philippine Eutropis, which suggested the endemic radiation was composed of five species (one of which was composed of two subspecies), we demonstrate that this group includes at least 14 distinct evolutionary lineages, with potential for additional diversity to be discovered pending further study.

Are you more than the sum of your parents' genes? Phenotypic plasticity in a clonal vertebrate and F1 hybrids of its parental species.

All known vertebrate clones have originated from hybridization events and some have produced distinct evolutionary lineages via hybrid speciation. Amazon mollies (Poecilia formosa) present an excellent study system to investigate how clonal species have adapted to heterogeneous environments because they are the product of a single hybridization event between male sailfin mollies (Poecilia latipinna) and female Atlantic mollies (Poecilia mexicana). Here, we ask whether the hybrid species differs from the combination of its parental species' genes in its plastic response to different environments. Using a three-way factorial design, we exposed neonates produced by Amazon mollies and reciprocal F1 hybrid crosses to different thermal (24°C and 29°C) and salinity (0/2, 12, and 20 ppt) regimes. We measured various ontogenetic and life history characteristics across the life span of females. Our major results were as follows: (1) Reaction norms of growth and maturation to temperature and salinity are quite similar between the two hybrid crosses; (2) Amazon molly reaction norms were qualitatively different than the P. latipinna male and P. mexicana female (L×M) hybrids for the ontogenetic variables; (3) Amazon molly reaction norms in reproductive traits were also quite different from L×M hybrids; and (4) The reaction norms of net fertility were very different between Amazon mollies and L×M hybrids. We conclude that best locale for Amazon mollies is not the best locale for hybrids, which suggests that Amazon mollies are not just an unmodified mix of parental genes but instead have adapted to the variable environments in which they are found. Hybridization resulting in asexuality may represent an underappreciated mechanism of speciation because the unlikely events required to produce such hybrids rarely occur and is dependent upon the genetic distance between parental species.

Taxonomic status of Chinese blue sheep (Pseudois nayaur): new evidence of a distinct subspecies.

The blue sheep is an endemic species to the Qinghai-Tibet Plateau and surrounding regions. It has been regarded as having 2 subspecies: Pseudois nayaur nayaur and P. n. szechuanensis. However, such a classification remains controversial. Herein, we analyze 10 microsatellite loci and part of the mitochondrial control region for clarification in such taxonomic debates. We use samples from 168 individuals from 6 geographic populations covering almost all the distribution areas of the species in China to carry out comparisons. Phylogenetic trees derived from both the microsatellite and mitochondrial markers combined with the discriminant analysis of principal components (DAPC) and the STRUCTURE analysis reveal that the individuals in the Helan Mountains are well grouped with a distinct evolutionary lineage and are significantly different from the other populations of P. n. szechuanensis according to Fst values, implying that this isolated population should be categorized as a valid subspecies; namely, Pseudois nayaur alashanicus. The isolation-by-distance (IBD) analysis shows a significant positive relationship between genetic and geographical distances among the populations.