Interbreeding among deeply divergent mitochondrial lineages in the American cockroach (Periplaneta americana)

PyKleeBarcode: Enabling representation of the whole animal kingdom in information space

As biological sequence databases continue growing, so do the insight that they promise to shed on the shape of the genetic diversity of life. However, to fulfil this promise the software must remain usable, be able to accommodate a large amount of data and allow use of modern high performance computing infrastructure. In this study we present a reimplementation as well as an extension of a technique using indicator vectors to compute and visualize similarities between sets of nucleotide sequences. We have a flexible and easy to use python program relying on standard and open-source libraries. Our tool allows analysis of very large complement of sequences using code parallelization, as well as by providing routines to split a computational task in smaller and manageable subtasks whose results are then merged. This implementation also facilitates adding new sequences into an indicator vector-based representation without re-computing the whole set. The efficient synthesis of data into knowledge is no trivial matter given the size and rapid growth of biological sequence databases. Based on previous results regarding the properties of indicator vectors, the open-source approach proposed here efficiently and flexibly supports comparative analysis of genetic diversity at a large scale. Our software is freely available at: https://github.com/WandrilleD/pyKleeBarcode.

Multiple invasions, Wolbachia and human-aided transport drive the genetic variability of Aedes albopictus in the Iberian Peninsula

The Asian tiger mosquito, Aedes albopictus, is one of the most invasive species in the world. Native to the tropical forests of Southeast Asia, over the past 30 years it has rapidly spread throughout tropical and temperate regions of the world. Its dramatic expansion has resulted in public health concerns as a consequence of its vector competence for at least 16 viruses. Previous studies showed that Ae. albopictus spread has been facilitated by human-mediated transportation, but much remains unknown about how this has affected its genetic attributes. Here we examined the factors that contributed to shaping the current genetic constitution of Ae. albopictus in the Iberian Peninsula, where the species was first found in 2004, by combining population genetics and Bayesian modelling. We found that both mitochondrial and nuclear DNA markers showed a lack of genetic structure and the presence of worldwide dominant haplotypes, suggesting regular introductions from abroad. Mitochondrial DNA showed little genetic diversity compared to nuclear DNA, likely explained by infection with maternally transmitted bacteria of the genus Wolbachia. Multilevel models revealed that greater mosquito fluxes (estimated from commuting patterns and tiger mosquito population distribution) and spatial proximity between sampling sites were associated with lower nuclear genetic distance, suggesting that rapid short- and medium-distance dispersal is facilitated by humans through vehicular traffic. This study highlights the significant role of human transportation in shaping the genetic attributes of Ae. albopictus and promoting regional gene flow, and underscores the need for a territorially integrated surveillance across scales of this disease-carrying mosquito.

Establishment of two new Anaplecta species (Blattodea, Blattoidea, Anaplectidae) based on morphological and COI data with an additional description of Anaplectafurcata Deng & Che, 2020

Based on morphological characteristics, including male and female genitalia, combined with DNA barcodes, two new species, Anaplectacircinalis Deng & Che, sp. nov. and Anaplectabihamata Deng & Che, sp. nov., are described in detail. Additional information on the female genitalia of Anaplectafurcata Deng & Che, 2020 is also provided. Photographs of external morphology and caudal anatomy of these species, as well as a key to the Chinese Anaplecta species, are provided.

Revealing the millipede and other soil-macrofaunal biodiversity in Hong Kong using a citizen science approach

Background

Soil biodiversity plays important roles in nutrient recycling in both the environment and agriculture. However, they are generally understudied worldwide. To reveal the diversity of soil macrofauna in Hong Kong, here we initiated a citizen science project involving university, non-governmental organisations and secondary school students and teachers. It is envisioned that the citizen science approach used in this study could be used as a demonstration to future biodiversity sampling and monitoring studies.

New information

Throughout a year of monitoring and species sampling across different localities in Hong Kong, 150 soil macrofaunal morphospecies were collected. Eighty five of them were further identified by morphology and DNA barcoding was assigned to each identified morphospecies, yielding a total of 646 DNA barcodes, with new millipede sequences deposited to the GenBank. The soil macrofauna morphospecies in Hong Kong found in this study are mainly dominated by millipedes (23 out of 150) and oligochaetes (15 out of 150). Amongst the twenty three identified millipedes, two polyxenid millipedes, Monographisqueenslandica Huynh & Veenstra, 2013 and Alloproctoidesremyi Marquet and Condé, 1950 are first recorded in Hong Kong. Information has been curated on an online platform and database (http://biodiversity.sls.cuhk.edu.hk/millipedes). A postcard summarising the findings of millipedes in Hong Kong has also been made as a souvenir and distributed to citizen participants. The identified macrofauna morphospecies and their 646 DNA barcodes in this study established a solid foundation for further research in soil biodiversity.

Molecular Phylogenetics of Physa acuta (Pulmonata: Basommatophora): an Invasive species in Central Punjab Pakistan

Physids belong to Class Gastropoda; belong to Phylum Mollusca and being bioindicators, intermediate hosts of parasites and pests hold a key position in the ecosystem. There are three species of Genus Physa i.e. P. fontinalis, Physa acuta and P. gyrina water bodies of Central Punjab and were characterized on the basis of molecular markers High level of genetic diversity was revealed by polymorphic RAPD, however SSR markers were not amplified. The multivariate analysis revealed polymorphism ranging from 9.09 percent to 50 percent among the three Physid species. Total number of 79 loci were observed for the three species under study and 24 loci were observed to be polymorphic. These RAPD fragment(s) can be developed into co dominant markers (SCAR) by cloning and can be further sequenced for the development of the Physa species specific markers to identify the introduced and native species in Pakistan.

A remarkable legion of guests: Diversity and host specificity of army ant symbionts

Tropical rainforests are among the most diverse biomes on Earth. While species inventories are far from complete for any tropical rainforest, even less is known about the intricate species interactions that form the basis of these ecological communities. One fascinating but poorly studied example are the symbiotic associations between army ants and their rich assemblages of parasitic arthropod guests. Hundreds of these guests, or myrmecophiles, have been taxonomically described. However, because previous work has mainly been based on haphazard collections from disjunct populations, it remains challenging to define species boundaries. We therefore know little about the species richness, abundance and host specificity of most guests in any given population, which is crucial to understand co-evolutionary and ecological dynamics. Here, we report a quantitative community survey of myrmecophiles parasitizing the six sympatric Eciton army ant species in a Costa Rican rainforest. Combining DNA barcoding with morphological identification of over 2,000 specimens, we discovered 62 species, including 49 beetles, 11 flies, one millipede and one silverfish. At least 14 of these species were new to science. Ecological network analysis revealed a clear signal of host partitioning, and each Eciton species was host to both specialists and generalists. These varying degrees in host specificities translated into a moderate level of network specificity, highlighting the system's level of biotic pluralism in terms of biodiversity and interaction diversity. By providing vouchered DNA barcodes for army ant guest species, this study provides a baseline for future work on co-evolutionary and ecological dynamics in these species-rich host-symbiont networks across the Neotropical realm.

Species diversity revealed in Sigmella Hebard, 1929 (Blattodea, ectobiidae) based on morphology and four molecular species delimitation methods

Cockroaches are one of the major decomposers involved in biogeochemical cycles. Cockroaches have an amazing amount of diversity, but most of them remain unknown due to the shortage of the trained taxonomists and the limitations of morphology-based identification. We obtained 49 COI sequences (including 42 novel sequences) and 32 novel 28S sequences for 5 Sigmella morphospecies collected from 11 localities. Three are new to science: Sigmella digitalis sp. nov., Sigmella exserta sp. nov. and Sigmella normalis sp. nov. Based on four species delimitation methods (ABGD, GMYC, BINs and bPTP), a total of 6 molecular operational taxonomic units (MOTUs) were recovered for 5 morphospecies. These were then confirmed by tree building methods using COI and combined data (COI and 28S). We detected more than one MOTU in the morphospecies S. digitalis sp. nov., which can indicate genetic diversity. Detailed morphological evidence for each MOTU is provided to confirm these slight variations and we conclude that natural barriers are likely the main cause of genetic diversity.

Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers

The American cockroach (Periplaneta americana) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of P. americana. Our study analyzed 1,053 P. americana and other Periplaneta species' samples from different locations in China and the United States. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of P. americana and 20 haplotypes of the other Periplaneta species accurately identified P. americana with a barcoding threshold of 5.1%. To identify the population genetic structure of P. americana, we investigated wingless gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. The analysis of molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that P. americana had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of P. americana. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct P. americana haplotype groups, showing four ancient maternal lineages of P. americana in China and the United States.

Genetic Diversity of Blattella germanica Isolates from Central China based on Mitochondrial Genes

Background:

Blattella germanica is a widespread urban invader insect that can spread numerous types of human pathogens, including bacteria, fungi, and protozoa. Despite the medical significance of B. germanica, the genetic diversity of this species has not been investigated across its wide geographical distribution in China.

Objective:

In this study, the genetic variation of B. germanica was evaluated in central China.

Methods:

Fragments of the mitochondrial cytochrome c oxidase subunit I (COI) gene and the 16S rRNA gene were amplified in 36 B. germanica isolates from 7 regions. The sequence data for COI and 16S rRNA genes were analyzed using bioinformatics methods.

Results:

In total, 13 haplotypes were found among the concatenated sequences. Each sampled population, and the total population, had high haplotype diversity (Hd) that was accompanied by low nucleotide diversity (Pi). Molecular genetic variation analysis indicated that 84.33% of the genetic variation derived from intra-region sequences. Phylogenetic analysis indicated that the B. germanica isolates from central China should be classified as a single population. Demographic analysis rejected the hypothesis of sudden population expansion of the B. germanica population.

Conclusion:

The 36 isolates of B. germanica sampled in this study had high genetic variation and belonged to the same species. They should be classified as a single population. The mismatch distribution analysis and BSP analysis did not support a demographic population expansion of the B. germanica population, which provided useful knowledge for monitoring changes in parasite populations for future control strategies.

Genetic Diversity and Wolbachia Infection Patterns in a Globally Distributed Invasive Ant

Understanding the phylogeographic history of an invasive species may facilitate reconstructing the history and routes of its invasion. The longhorn crazy ant, Paratrechina longicornis, is a ubiquitous agricultural and household pest throughout much of the tropics and subtropics, but little is known about the history of its spread. Here, we examine worldwide genetic variation in P. longicornis and its associated Wolbachia bacterial symbionts. Analyses of mtDNA sequences of 248 P. longicornis workers (one per colony) from 13 geographic regions reveal two highly diverged mtDNA clades that co-occur in most of the geographic regions. These two mtDNA clades are associated with different Wolbachia infection patterns, but are not congruent with patterns of nDNA (microsatellite) variation. Multilocus sequence typing reveals two distinct Wolbachia strains in P. longicornis, namely, wLonA and wLonF. The evolutionary histories of these two strains differ; wLonA appears to be primarily transmitted maternally, and patterns of mtDNA and nDNA variation and wLonA infection status are consistent with a relatively recent Wolbachia-induced selective sweep. In contrast, the observed patterns of mtDNA variation and wLonF infections suggest frequent horizontal transfer and losses of wLonF infections. The lack of nDNA structure among sampled geographic regions coupled with the finding that numerous mtDNA haplotypes are shared among regions implies that inadvertent long-distance movement through human commerce is common in P. longicornis and has shaped the genetic structure of this invasive ant worldwide.

Species-level predation network uncovers high prey specificity in a Neotropical army ant community

Army ants are among the top arthropod predators and considered keystone species in tropical ecosystems. During daily mass raids with many thousand workers, army ants hunt live prey, likely exerting strong top-down control on prey species. Many tropical sites exhibit a high army ant species diversity (>20 species), suggesting that sympatric species partition the available prey niches. However, whether and to what extent this is achieved has not been intensively studied yet. We therefore conducted a large-scale diet survey of a community of surface-raiding army ants at La Selva Biological Station in Costa Rica. We systematically collected 3,262 prey items from eleven army ant species (genera Eciton, Nomamyrmex and Neivamyrmex). Prey items were classified as ant prey or non-ant prey. The prey nearly exclusively consisted of other ants (98%), and most booty was ant brood (87%). Using morphological characters and DNA barcoding, we identified a total of 1,103 ant prey specimens to the species level. One hundred twenty-nine ant species were detected among the army ant prey, representing about 30% of the known local ant diversity. Using weighted bipartite network analyses, we show that prey specialization in army ants is unexpectedly high and prey niche overlap very small. Besides food niche differentiation, we uncovered a spatiotemporal niche differentiation in army ant raid activity. We discuss competition-driven multidimensional niche differentiation and predator-prey arms races as possible mechanisms underlying prey specialization in army ants. By combining systematic prey sampling with species-level prey identification and network analyses, our integrative approach can guide future research by portraying how predator-prey interactions in complex communities can be reliably studied, even in cases where morphological prey identification is infeasible.

Chemical and behavioral integration of army ant-associated rove beetles - a comparison between specialists and generalists

Host-symbiont interactions are embedded in ecological communities and range from unspecific to highly specific relationships. Army ants and their arthropod guests represent a fascinating example of species-rich host-symbiont associations where host specificity ranges across the entire generalist - specialist continuum. In the present study, we compared the behavioral and chemical integration mechanisms of two extremes of the generalist - specialist continuum: generalist ant-predators in the genus Tetradonia (Staphylinidae: Aleocharinae: Athetini), and specialist ant-mimics in the genera Ecitomorpha and Ecitophya (Staphylinidae: Aleocharinae: Ecitocharini). Similar to a previous study of Tetradonia beetles, we combined DNA barcoding with morphological studies to define species boundaries in ant-mimicking beetles. This approach found four ant-mimicking species at our study site at La Selva Biological Station in Costa Rica. Community sampling of Eciton army ant parasites revealed that ant-mimicking beetles were perfect host specialists, each beetle species being associated with a single Eciton species. These specialists were seamlessly integrated into the host colony, while generalists avoided physical contact to host ants in behavioral assays. Analysis of the ants' nestmate recognition cues, i.e. cuticular hydrocarbons (CHCs), showed close similarity in CHC composition and CHC concentration between specialists and Eciton burchellii foreli host ants. On the contrary, the chemical profiles of generalists matched host profiles less well, indicating that high accuracy in chemical host resemblance is only accomplished by socially integrated species. Considering the interplay between behavior, morphology, and cuticular chemistry, specialists but not generalists have cracked the ants' social code with respect to various sensory modalities. Our results support the long-standing idea that the evolution of host-specialization in parasites is a trade-off between the range of potential host species and the level of specialization on any particular host.

Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China

We collected Ectobiidae cockroach specimens from 44 locations in the south of the Yangtze valley. We obtained 297 COI sequences specimens and carried out phylogenetic and divergence dating analyses, as well as species delimitation analysis using a General Mixed Yule Coalescent (GMYC) framework. The intraspecific and interspecific sequence divergence in Ectobiidae cockroaches ranged from 0.0 to 7.0% and 4.6 to 30.8%, respectively. GMYC analysis resulted in 53 (confidence interval: 37-65) entities (likelihood ratio = 103.63) including 14 downloaded species. The COI GMYC groups partly corresponded to the ectobiid species and 52 ectobiid species were delimited successfully based on the combination of GMYC result with morphological information. We used the molecular data and 6 cockroach fossil calibrations to obtain a preliminary estimate of the timescale of ectobiid evolution. The major subfamilies in the group were found to have diverged between ~125-110 Ma, and morphospecies pairs were found to have diverged ~10 or more Ma.

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae)

Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae). Systematic community sampling of 58 colonies of the six local Eciton species at La Selva Biological Station, Costa Rica, combined with an integrative taxonomic approach, allowed us to uncover species diversity, host specificity, and co-occurrence patterns of symbionts in unprecedented detail. We used an integrative taxonomic approach combining morphological and genetic analyses, to delineate species boundaries. Mitochondrial DNA barcodes were analyzed for 362 Tetradonia specimens, and additional nuclear markers for a subset of 88 specimens. All analyses supported the presence of five Tetradonia species, including two species new to science. Host specificity is highly variable across species, ranging from generalists such as T. laticeps, which parasitizes all six local Eciton species, to specialists such as T. lizonae, which primarily parasitizes a single species, E. hamatum. Here we provide a dichotomous key along with diagnostic molecular characters for identification of Tetradonia species at La Selva Biological Station. By reliably assessing biodiversity and providing tools for species identification, we hope to set the baseline for future studies of the ecological and evolutionary dynamics in these species-rich host-symbiont networks.

Cryptic diversity, high host specificity and reproductive synchronization in army ant-associated Vatesus beetles

Army ants and their arthropod symbionts represent one of the most species-rich animal associations on Earth, and constitute a fascinating example of diverse host-symbiont interaction networks. However, despite decades of research, our knowledge of army ant symbionts remains fragmentary due to taxonomic ambiguity and the inability to study army ants in the laboratory. Here, we present an integrative approach that allows us to reliably determine species boundaries, assess biodiversity, match different developmental stages and sexes, and to study the life cycles of army ant symbionts. This approach is based on a combination of community sampling, DNA barcoding, morphology and physiology. As a test case, we applied this approach to the staphylinid beetle genus Vatesus and its different Eciton army ant host species at La Selva Biological Station, Costa Rica. DNA barcoding led to the discovery of cryptic biodiversity and, in combination with extensive community sampling, revealed strict host partitioning with no overlap in host range. Using DNA barcoding, we were also able to match the larval stages of all focal Vatesus species. In combination with studies of female reproductive physiology, this allowed us to reconstruct almost the complete life cycles of the different beetle species. We show that Vatesus beetles are highly adapted to the symbiosis with army ants, in that their reproduction and larval development are synchronized with the stereotypical reproductive and behavioural cycles of their host colonies. Our approach can now be used to study army ant-symbiont communities more broadly, and to obtain novel insights into co-evolutionary and ecological dynamics in species-rich host-symbiont systems.

Generation-based life table analysis reveals manifold effects of inbreeding on the population fitness in Plutella xylostella

Understanding how inbreeding affects fitness is biologically important for conservation and pest management. Despite being a worldwide pest of many economically important cruciferous crops, the influence of inbreeding on diamondback moth, Plutella xylostella (L.), populations is currently unknown. Using age-stage-specific life tables, we quantified the inbreeding effects on fitness-related traits and demographic parameters of P. xylostella. Egg hatching rate, survival and fecundity of the inbred line significantly declined compared to those of the outbred line over time. The inbred P. xylostella line showed significantly lower intrinsic rate of increase (r), net reproduction rate (R₀), and finite increase rate (λ), and increasing generation time (T). Inbreeding effects vary with developmental stages and the fitness-related traits can be profoundly affected by the duration of inbreeding. Our work provides a foundation for further studies on molecular and genetic bases of the inbreeding depression for P. xylostella.