Distinct Genetic Lineages Research Articles

Multi-character taxonomic review, systematics, and biogeography of the Black-capped/Tawny-bellied Screech Owl (emMegascops/em ematricapilla/em-emM. watsonii/em) complex (Aves: Strigidae).

Megascops is the most species-rich owl genus in the New World, with 21 species currently recognized. Phylogenetic relationships within this genus are notoriously difficult to establish due to the considerable plumage similarity among species and polymorphism within species. Previous studies have suggested that the widespread lowland Amazonian M. watsonii might include more than one species, and that the Atlantic Forest endemic M. atricapilla is closely related to the M. watsonii complex, but these relationships are as yet poorly understood. A recently published phylogeny of Megascops demonstrated that M. watsonii is paraphyletic with respect to M. atricapilla and that genetic divergences among some populations of M. watsonii are equal to or surpass the degree of differentiation between some M. watsonii and M. atricapilla. To shed light on the taxonomic status of these species and populations within them, we conducted a multi-character study based on molecular, morphological, and vocal characters. We sequenced three mitochondrial (cytb, CO1 and ND2) and three nuclear genes (BF5, CHD and MUSK) for 49 specimens, covering most of the geographic ranges of M. watsonii and M. atricapilla, and used these sequences to estimate phylogenies under alternative Bayesian, Maximum Likelihood, and multilocus coalescent species tree approaches. We studied 252 specimens and vocal parameters from 83 recordings belonging to 65 individuals, distributed throughout the ranges of M. watsonii and M. atricapilla. We used Discriminant Function Analysis (DFA) to analyze both morphometric and vocal data, and a pairwise diagnostic test to evaluate the significance of vocal differences between distinct genetic lineages. Phylogenetic analyses consistently recovered six statistically well-supported clades whose relationships are not entirely in agreement with currently recognized species limits in M. watsonii and M. atricapilla. Morphometric analyses did not detect significant differences among clades. High plumage variation among individuals within clades was usually associated with the presence of two or more color morphs. By contrast, vocal analyses detected significant differentiation among some clades but considerable overlap among others, with some lineages (particularly the most widespread one) exhibiting significant regional variation. The combined results allow for a redefinition of species limits in both M. watsonii and M. atricapilla, with the recognition of four additional species, two of which we describe here as new. We estimated most cladogenesis in the Megascops atricapilla-M. watsonii complex as having taken place during the Plio-Pleistocene, with the development of the modern Amazonian and São Francisco drainages and the expansion and retraction of forest biomes during interglacial and glacial periods as likely events accounting for this relatively recent burst of diversification.

Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap.

Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C4 and C4 groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C4 and non-C4 types never grew together, and the C4 type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.

Hidden diversity of the most basal tapeworms (Cestoda, Gyrocotylidea), the enigmatic parasites of holocephalans (Chimaeriformes)

Gyrocotylideans are evolutionary ancient parasitic flatworms, and like their hosts—a relict group of holocephalan fishes (Chimaeriformes)—they are considered to be “living fossils” of a vanished past. However, the species diversity, host associations and biogeography of these most basal tapeworms are poorly known. Herein, we provide evidence of a conspicuous contrast between the genetic and morphological data based on an examination of newly collected and properly processed Gyrocotyle specimens (hologenophores) isolated from holocephalans off Taiwan and Argentina. Our molecular data, inferred from three genes (COI, 28S rRNA, 18S rRNA), showed unexpected genetic interrelationships among isolates of the genus Gyrocotyle, because each of the four genotypes from Taiwan clustered with isolates of distinct gyrocotylideans from the North Atlantic. Three genotypes of Gyrocotyle from Taiwan were morphologically almost indistinguishable from each other but represented distinct genetic lineages; a single specimen of Gyrocotyle sp. genotype 4 exhibited a clear genetic and morphological distinctness, though its formal description as a new species would be premature. Additionally, specimens of Gyrocotyle rugosa Diesing, 1850, from the type host Callorhinchus callorynchus from Argentina, provided the first genetic data on the type species of the genus and enabled us to characterise it, which is necessary for future taxonomic studies. The finding of some specimens of Gyrocotyle sp. genotype 3 in Chimaera phantasma, and another one in C. cf. argiloba, together with the putative conspecificity of an unidentified gyrocotylidean from Callorhinchus milii off Australia and G. rugosa from C. callorynchus off Argentina, represent evidence that one gyrocotylidean species may parasitise more than one holocephalan host species. Existing taxonomic problems and conflicts between morphological and molecular data on species of Gyrocotyle can only be resolved if hologenophores from type hosts and localities of nominal taxa are properly characterised genetically and morphologically.

Cryptic genetic lineages of a colonial ascidian host distinct microbiomes

AbstractColour variation in marine invertebrates is typically attributed to intraspecific variability; however, the use of molecular tools to investigate its genetic basis has uncovered many instances of cryptic speciation. The colonial ascidian Distaplia bermudensis occurs in a wide array of colour morphs, ranging from all white to a dark blue tunic with yellow siphon apertures; yet careful observations of zooid and larval morphologies have not revealed any consistent difference among these colour morphs. In this study, we sampled the 5 main colour morph groupings of D. bermudensis from Wilmington, North Carolina (USA) and sequenced fragments of the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear 18S rRNA genes. Analyses of both genes revealed the presence of two distinct genetic lineages that corresponded to unique colour morphology groupings. We further characterized symbiotic microbial communities for four samples from each lineage by high‐throughput sequencing of partial 16S rRNA genes. Each genetic lineage also harboured unique symbiont communities that differed significantly in diversity and structure. Thus, the two genetic lineages detected herein corresponded to unique colour morphs and microbial communities, indicating that two distinct species coexist under the same scientific name. Further, our study reports the utility of symbiont profiling in resolving the taxonomic status of phenotypically variable ascidian species.

Mitochondrial dna diversity of crossbanded barb Puntioplites bulu (Bleeker, 1851) from natural populations in peninsular Malaysia

Puntoplites bulu is a freshwater Cyprinidae and widely distributed in Southeast Asia. It has attracted considerable interest due to high demand and price. However, an apparent decline in its distribution and abundance is observed and this is due to several factors, such as habitat degradation, pollution, and overfishing. Intraspecific variation of P.bulu from three major rivers in Peninsular Malaysia were determined based on genetic divergence by using mtDNA Cyt b. Two distinct genetic lineages were apparent viz Central West and East Peninsular Malaysia with natural barriers (the Titiwangsa Range) acted as natural dividers between these two lineages. Alternatively, the close genetic relation and haplotype sharing that were observed between Perak and Kelantan populations could be due to human translocations. Further, haplotype sharing between Kelantan and Pahang populations revealed the migration ability of P. bulu through ancient connectivity. These findings provide an important base study for initiating a selective breeding program

Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa

BackgroundPlant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity and diversity of TEs. Here, we combined common garden experiment with short-read sequencing to investigate genomic abundance and expression of 2245 consensus TE sequences (containing retrotransposons and DNA transposons) in an alpine environment in Arabidopsis arenosa. To disentangle general trends from local differentiation, we leveraged four foothill-alpine population pairs from different mountain regions. Seeds of each of the eight populations were raised under four treatments that differed in temperature and irradiance, two factors varying with elevation. RNA-seq analysis was performed on leaves of young plants to test for the effect of elevation and subsequently of temperature and irradiance on expression of TE sequences.ResultsGenomic abundance of the 2245 consensus TE sequences varied greatly between the mountain regions in line with neutral divergence among the regions, representing distinct genetic lineages of A. arenosa. Accounting for intraspecific variation in abundance, we found consistent transcriptomic response for some TE sequences across the different pairs of foothill-alpine populations suggesting parallelism in TE expression. In particular expression of retrotransposon LTR Copia (e.g. Ivana and Ale clades) and LTR Gypsy (e.g. Athila and CRM clades) but also non-LTR LINE or DNA transposon TIR MuDR consistently varied with elevation of origin. TE sequences responding specifically to temperature and irradiance belonged to the same classes as well as additional TE clades containing potentially stress-responsive elements (e.g. LTR Copia Sire and Tar, LTR Gypsy Reina).ConclusionsOur study demonstrated that the A. arenosa genome harbours a considerable diversity of TE sequences whose abundance and expression response varies across its native range. Some TE clades may contain transcriptionally active elements responding to a natural environmental gradient. This may further contribute to genetic variation between populations and may ultimately provide new regulatory mechanisms to face environmental challenges.

Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene.

Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.

Pilot Fecal DNA Barcoding on Selected Fruit Bats in Davao City, Philippines

The “Species from Feces” DNA barcoding offers new opportunities to study the challenging taxonomy and systematics of Philippine bats using a minimally-invasive strategy that employs a short 200- bp mitochondrial encoded cytochrome c oxidase I (mt COI) sequence. A pilot application of the technique to five species of fruit bats collected from Davao City, Philippines revealed accurate species identification and the extended ability to assess genetic diversity and evolutionary relationships. The 95–100% sequence identity matched with the field identification of bats, including the endemic Ptenochirus jagori, although only 62% of the samples could be sequenced. A decreasing trend in genetic diversity was noted from widespread bat species such as Rousettus amplexicaudatus, Cynopterus brachyotis, and Macroglossus minimus to species with limited geographic distribution (e.g. P. jagori) or possible recent colonization (e.g. Eonycteris spelaea). Genetic diversity, principal coordinate analysis (PCoA), and phylogenetic analysis also showed distinct genetic lineages of C. brachyotis, R. amplexicaudatus, and M. minimus from their conspecifics outside the Philippines, while E. spelaea and the endemic P. jagori exhibited genetic homogeneity. The findings on genetic diversity and relationships were consistent with previous studies using longer COI segment or other biomarkers. In conclusion, the Species from Feces DNA barcoding presents a minimally invasive and pragmatic approach to explore bat assemblages with the additional utility to examine genetic structures and relationships, which may be used to support studies on diversity, evolution, and biogeography, thereby rapidly facilitate conservation initiatives.

A New Species of Alopoglossus Boulenger (1885) (Squamata, Alopoglossidae) from the Lowlands of the Eastern Guiana Shield, with Assessment of the Taxonomic Status of A. copii surinamensis

Two species of Alopoglossus (A. angulatus and A. meloi) were recognized to occur in the Guiana Shield lowlands, northeastern Amazonia. A third group of populations forming a distinct genetic lineage related to Alopoglossus avilapiresae was recently documented in the region. The Guiana Shield lowlands area also encompasses the type locality of Alopoglossus copii surinamensis (currently considered a synonym of A. angulatus). Aiming at describing a possible new species of Alopoglossus from the Guiana Shield and evaluating the taxonomic status of A. copii surinamensis, we analyzed variation in scutellation and morphometrics of the two nominal species of Alopoglossus occurring in the Guiana Shield and A. avilapiresae, which was recovered as the sister clade of the new Guiana Shield lineage, by examining 361 specimens from French Guiana, Brazil, Suriname, Guyana, Colombia, Ecuador, and Peru. Our results revealed a distinct combination of diagnostic characters that supports the description of specimens displaying the third Guiana Shield lineage as a new species. The new species is also distinct from A. copii surinamensis that we retain under a synonym of A. angulatus after examination of all species of the angulatus group and by considering updated diagnostic characters. The new taxon described here increases the total number of known species of Alopoglossus to 15.

A fine-scale map of genome-wide recombination in divergent Escherichia coli population.

Recombination is one of the most important molecular mechanisms of prokaryotic genome evolution, but its exact roles are still in debate. Here we try to infer genome-wide recombination within a species, utilizing a dataset of 149 complete genomes of Escherichia coli from diverse animal hosts and geographic origins, including 45 in-house sequenced with the single-molecular real-time platform. Two major clades identified based on physiological, clinical and ecological characteristics form distinct genetic lineages based on scarcity of interclade gene exchanges. By defining gene-based syntenies for genomic segments within and between the two clades, we build a fine-scale recombination map for this representative global E. coli population. The map suggests extensive within-clade recombination that often breaks physical linkages among individual genes but seldom interrupts the structure of genome organizational frameworks as well as primary metabolic portfolios supported by the framework integrity, possibly due to strong natural selection for both physiological compatibility and ecological fitness. In contrast, the between-clade recombination declines drastically when phylogenetic distance increases to the extent where a 10-fold reduction can be observed, establishing a firm genetic barrier between clades. Our empirical data suggest a critical role for such recombination events in the early stage of speciation where recombination rate is associated with phylogenetic distance in addition to sequence and gene variations. The extensive intraclade recombination binds sister strains into a quasisexual group and optimizes genes or alleles to streamline physiological activities, whereas the sharply declined interclade recombination split the population into clades adaptive to divergent ecological niches.

Multilocus Genotyping Reveals New Molecular Markers for Differentiating Distinct Genetic Lineages among “Candidatus Phytoplasma Solani” Strains Associated with Grapevine Bois Noir

Grapevine Bois noir (BN) is associated with infection by “Candidatus Phytoplasma solani” (CaPsol). In this study, an array of CaPsol strains was identified from 142 symptomatic grapevines in vineyards of northern, central, and southern Italy and North Macedonia. Molecular typing of the CaPsol strains was carried out by analysis of genes encoding 16S rRNA and translation elongation factor EF-Tu, as well as eight other previously uncharacterized genomic fragments. Strains of tuf-type a and b were found to be differentially distributed in the examined geographic regions in correlation with the prevalence of nettle and bindweed. Two sequence variants were identified in each of the four genomic segments harboring hlyC, cbiQ-glyA, trxA-truB-rsuA, and rplS-tyrS-csdB, respectively. Fifteen CaPsol lineages were identified based on distinct combinations of sequence variations within these genetic loci. Each CaPsol lineage exhibited a unique collective restriction fragment length polymorphism (RFLP) pattern and differed from each other in geographic distribution, probably in relation to the diverse ecological complexity of vineyards and their surroundings. This RFLP-based typing method could be a useful tool for investigating the ecology of CaPsol and the epidemiology of its associated diseases. Phylogenetic analyses highlighted that the sequence variants of the gene hlyC, which encodes a hemolysin III-like protein, separated into two clusters consistent with the separation of two distinct lineages on the basis of tufB gene sequences. Alignments of deduced full protein sequences of elongation factor-Tu (tufB gene) and hemolysin III-like protein (hlyC gene) revealed the presence of critical amino acid substitutions distinguishing CaPsol strains of tuf-type a and b. Findings from the present study provide new insights into the genetic diversity and ecology of CaPsol populations in vineyards.

Understanding the genetic diversity of the guayabillo (Psidium galapageium), an endemic plant of the Galapagos Islands

Oceanic archipelagos are known to host a variety of endemic plant species. The genetic diversity and structure of these species are important indicators of their evolutionary history and can have consequences on the implementation of appropriate conservation strategies. A comprehensive consideration of the role of their natural history, as well as the landscape features and the geological history of the islands themselves are required to adequately understand the geographic patterns inferred from genetic data. Such is the case for guayabillo (Psidium galapageium), an understudied endemic plant from the Galapagos Islands with important ecological and economic roles. In this study we designed and evaluated 13 informative SSR markers and used them to investigate the genetic diversity, population structure and connectivity of the guayabillo populations from San Cristobal, Isabela and Santa Cruz islands. A total of 208 guayabillo individuals were analyzed, revealing a strong population structure between islands and two distinct genetic lineages for the Santa Cruz population. Overall, the relatively high genetic diversity of the species could be explained by different biological, demographic and environmental factors. For guayabillo populations such as the one in San Cristobal, the history of human disturbance in their habitats might play an important role in explaining their reduced genetic diversity. The coexistence of two distinct lineages in Santa Cruz, with one of them sharing genetic similarities with individuals from San Cristobal, could be attributed to limited, unidirectional gene flow from the latter island to the former. Our findings highlight the complex population dynamics that shape the genetic diversity of species like the guayabillo, and emphasize the importance of a species’ evolution and natural history when interpreting its population genetics.

Multilocus and morphological analysis of south‐eastern Iberian Wall lizards (Squamata, Podarcis)

AbstractThe phylogenetic relationships among the wall lizards of the Podarcis hispanicus complex that inhabit the south‐east (SE) of the Iberian Peninsula and other lineages of the complex remain unclear. In this study, four mitochondrial and two nuclear markers were used to study genetic relationships within this complex. The phylogenetic analyses based on mtDNA gene trees constructed with ML and BI, and a species tree using *BEAST support three divergent clades in this region: the Valencia, Galera and Albacete/Murcia lineages. These three lineages were also corroborated in species delimitation analyses based on mtDNA using bPTP, mPTP, GMYC, ABGD and BAPS. Bayesian inference species delimitation method (BPP) based on both nuclear data and a combined data set (mtDNA + nuclear) showed high posterior probabilities for these three SE lineages (≥0.94) and another Bayesian analysis (STACEY) based on combined data set recovered the same three groups in this region. Divergence time dating of the species tree provided an estimated divergence of the Galera lineage from the other SE group (Podarcis vaucheri, (Albacete/Murcia, Valencia)) at 12.48 Ma. During this period, the Betic–Rifian arc was isolated, which could have caused the isolation of the Galera form distributed to the south of the Betic Corridor. Although lizards from the Albacete/Murcia and Galera lineage are morphologically similar, they clearly represent distinct genetic lineages. The noteworthy separation of the Galera lineage enables us to conclude that this lineage must be considered as a new full species.

Vicariance in a generalist fish parasite driven by climate and salinity tolerance of hosts.

Acanthocephalans are parasites with complex lifecycles that are important components of aquatic systems and are often model species for parasite-mediated host manipulation. Genetic characterization has recently resurrected Pomphorhynchus tereticollis as a distinct species from Pomphorhynchus laevis, with potential implications for fisheries management and host manipulation research. Morphological and molecular examinations of parasites from 7 English rivers across 9 fish species revealed that P. tereticollis was the only Pomphorhynchus parasite present in Britain, rather than P. laevis as previously recorded. Molecular analyses included two non-overlapping regions of the mitochondrial gene - cytochrome oxidase and generated 62 sequences for the shorter fragment (295 bp) and 74 for the larger fragment (583 bp). These were combined with 61 and 13 sequences respectively, from Genbank. A phylogenetic analysis using the two genetic regions and all the DNA sequences available for P. tereticollis identified two distinct genetic lineages in Britain. One lineage, possibly associated with cold water tolerant fish, potentially spread to the northern parts of Britain from the Baltic region via a northern route across the estuarine area of what is now the North Sea during the last Glaciation. The other lineage, associated with temperate freshwater fish, may have arrived later via the Rhine/Thames fluvial connection during the last glaciation or early Holocene when sea levels were low. These results raise important questions on this generalist parasite and its variously environmentally adapted hosts, and especially in relation to the consequences for parasite vicariance.

Population genetic structure of the giant panda staple food bamboo (Fargesia spathacea complex) and its taxonomic implications

AbstractThe taxonomy of woody bamboo presents many difficulties due to its long blooming interval and complex morphological variation. Whether the current taxonomy reflects genuine species divergence within woody bamboo is an intriguing question. The Fargesia spathacea Franch. complex comprises 15 closely related species with a sympatric distribution in China. Their classification has long been controversial because only a handful of vegetative traits are available, providing a good opportunity to explore the evolutionary relationships and genetic differentiation in woody bamboo. Here, we present a study involving 750 individuals from 39 representative populations in the F. spathacea complex using 14 simple sequence repeat markers. We found varying degrees of genetic diversity across populations of the F. spathacea complex (He = 0.07–0.81) and largely negative F‐values at the population level, implying an excess of heterozygotes in the populations. Phylogenetic analyses revealed that all populations were divided into two major groups (clusters A and B), with the majority of the 15 species representing distinct genetic lineages. Based on population genetic analysis along with morphological evidence, we confirmed the identity of three species (F. decurvata J. L. Lu, F. spathacea, and F. murielae Gamble) and suggested the invalidation of four other species (F. scabrida T. P. Yi, F. robusta T. P. Yi, F. denudata T. P. Yi F. murielae (Gamble) T. P. Yi, and F. nitida (Mitford) Keng f. ex T. P. Yi). The delimitation of the remaining eight species has yet to be explored. The analysis of ecological factors and spatial autocorrelation suggested that altitudinal differences might account for the distinct genetic divergence between the two major groups.

Mitochondrial DNA barcodes provide insight into the phylogeography and subspecies controversy in the widespread Neotropical white peacock butterfly,Anartia jatrophae(Nymphalidae: Nymphalinae)

AbstractThe validity of subspecies designations in the common and wide-ranging Neotropical white peacock butterfly, Anartia jatrophae, has been debated for decades and remains an unsettled and contentious taxonomic issue among lepidopterists. Originally described by Linnaeus in the mid-18th century from specimens obtained from northern South America (Suriname), subsequent authors proposed a variety of subspecies names based on differences in adult external morphology among geographical populations. Many of these differences, however, were subsequently found to occur seasonally within populations, leading some to conclude that only a single polymorphic species should be recognized. Here, we have analysed both new and publicly available mitochondrial DNA barcodes, obtained from specimens collected from southern USA to northern Argentina, to assess whether they could provide insight into this long-standing controversy. Our molecular analyses, using a combination of character-based (nucleotide composition), population genetic and phylogenetic approaches, indicated the presence of at least four distinct genetic lineages that we suggest are distinct at the subspecies level, namely A. j. jatrophae, A. j. luteipicta, A. j. saturata and A. j. semifusca. Justification for these assignments and the proposed geographical distribution of each subspecies within the Americas are discussed.

Little genetic distinction between varieties of Pinto Beardtongue (Penstemon bicolor, Plantaginaceae), a rare plant native to the Mojave Desert 1

Penstemon bicolor is a relatively rare, short-lived perennial herb of conservation concern and is found in the Mojave Desert and surrounding areas of southern Nevada, southeastern California, and northwestern Arizona. Two varieties of P. bicolor are named according to the color of their corolla: variety bicolor, the yellow or pink-colored form, and variety roseus, the magenta-colored form. The rarity of P. bicolor var. bicolor, coupled with its limited distribution, raises concerns about the genetic diversity present in the species, which is critical for the survival of species in the face of environmental stressors, such as habitat loss. Conservation management strategies for P. bicolor rely partially on the taxonomic status of variety bicolor and variety roseus; if these varieties are in fact distinct genetic lineages more appropriately defined as different species, then the implementation and urgency of management strategies would require updating accordingly. We analyzed amplified fragment length polymorphisms and inter-simple sequence repeats for 13 populations of P. bicolor from southern Nevada and northwestern Arizona to assess genetic diversity within the species and to identify the genetic distinctiveness, if any, between varieties. Our findings reveal surprisingly high levels of genetic diversity, in contrast to expectations for rare, perennial, outcrossing plants. Penstemon bicolor does, however, face ongoing threats of habitat destruction and potential local extirpation due to urbanization of the greater Las Vegas area, and we recommend that the current protective status of the species be maintained. Additionally, our analyses of differentiation failed to reveal genetic distinctiveness between varieties; we thus do not recommend that varieties of P. bicolor be elevated to species level.

Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico.

Pontoscolex corethrurus (Müller, 1857) is an invasive tropical earthworm, globally distributed. It reproduces through parthenogenesis, which theoretically results in low genetic diversity. The analysis of the population structure of P. corethrurus using molecular markers may significantly contribute to understanding the ecology and reproductive system of this earthworm species. This work assessed the genetic diversity and population structure of P. corethrurus with 34 polymorphic inter simple sequence repeat markers, covering four populations in tropical and temperate pastures from Veracruz State. Nuclear markers distinguished two genetic clusters, probably corresponding to two distinct genetic lineages. The number of clones detected in the AC population was lower than expected for a parthenogenetic species. Also, the apparent lack of differences in population structures related to the geographic region among the populations studied may indicate that human-mediated transference is prevalent in these areas. Still, most individuals apparently belong to lineage A, and only a few individuals seem to belong to the lineage B. Thus, the admixture signatures found among the four populations of P. corethrurus may have facilitated a successful invasion by directly increasing fitness. In summary, addressing the genetic variation of P. corethrurus with ISSR markers was a suitable approach, as it evidenced the genetic diversity and relationships in the populations evaluated.

First come, first served: Possible role for priority effects in marine populations under different degrees of dispersal potential

AbstractAimStudying clearly delineated populations in marine lakes, islands of sea, we investigated the interplay of habitat size, dispersal potential, and priority effects in shaping marine population genetic structure.LocationMarine lakes and coastal locations in Indonesia, Palau, Papua New Guinea and Australia.TaxonMussels (Mytilidae, Brachidontes spp.)MethodsPopulations were sampled from four coastal locations and 22 marine lakes of similar age (~8,000 years), yet differing in size (0.04–4.7 km2) and degree of connection to the adjacent sea. While some lakes are highly connected, allowing potential influx of larvae from the sea, others have very limited water exchange. We assessed the phylogeographical structure and demographic history using mitochondrial and nuclear DNA sequence data, and combined this with geometric morphometrics. The effects of lake characteristics on population genetic diversity and structure were tested using linear regression and Mantel tests.ResultsEach lake contained one of six distinct genetic lineages, which were characterized by deep phylogenetic splits and significant morphometric differences. These lineages likely represent separate species. The lineages showed similar demographic patterns, with lakes containing founder populations that rapidly expanded and diverged. Genetic diversity within lake populations was significantly correlated with lake area, but not with physical connection to the adjacent sea. Within lineages that occurred in multiple lakes there was strong population structure (average ΦST 0.65), which did not conform to an isolation‐by‐distance pattern or to the degree of dispersal potential.Main ConclusionsMarine lakes across a gradient of physical isolation show strong population structure and evidence for in situ divergence. We hypothesize that the observed genetic structure is the result of priority effects. In addition, reduction of habitat size appears to reduce genetic diversity, even at very small spatial scales. Our findings are relevant in the context of ongoing alterations to coastal hydrodynamics, which lead to habitat reduction and influence migration among populations at fine spatial scales.

Cryptic diversity in fruit fly, Zeugodacus isolatus (Hardy) (Diptera: Tephritidae)

Zeugodacus isolatus (Hardy) is a member of the Z. tau complex, a group of significant pest fruit flies. Therefore, fully understanding the taxonomy and biodiversity of this species-complex is of paramount importance for its effective subsequent management. In this study, morphological characters and molecular genetic data based on sequences of three genes were used to examine variations in Z. isolatus (Hardy) in Thailand. Median joining haplotype networks revealed two genetically divergent lineages (A and B) among members of Z. isolatus in Thailand. Morphological examinations revealed that these genetic lineages are clearly different in many characteristics including body size, postgena colors and scutum color patterns. Although they coexist and use the same host plant species, the distinct genetic lineages and differing morphological characters suggest that they are possibly reproductively isolated and different biological species.