Hidden island endemic species and their implications for cryptic speciation within soil arthropods

The distribution of species changes over time, and the current distribution of different species could result from distinct eco-evolutionary processes. Thus, investigating the spatiotemporal changes in the niche and geographic range of species is fundamental to understanding those processes and mechanisms shaping the current distributions of species. However, many studies only compared the current distribution and niche of the target species, ignoring the fact that the range shift of species is a dynamic process. Here, we reconstructed niche evolution and range dynamics of species to provide more information on related eco-evolutionary processes. We focused on a monophyletic species complex,Chrysanthemum zawadskiispecies complex, in which species occupy diverse habitats and exhibit different distribution patterns. Specifically, we investigated the niche breadth and overlap between lineages or species of the complex in geographic and environmental spaces. We then tested the phylogenetic signals for different climatic variables and estimated the niche of ancestral nodes on a time-calibrated phylogeny. Next, we used phyloclimatic modeling to reconstruct the dynamics of range shift for this complex. Our results show that this complex contains both specialist and generalist species, and niche diverges greatly among different species and intraspecific lineages of the complex. The moisture gradient may be the primary driver of the niche divergence of species in the complex. The reconstruction of ancestral distribution shows that this complex originated in the Qinling mountains and surrounding areas during the early Pliocene, and then diverged with the range expansion and niche evolution. Species of the complex have different range dynamics. Based on our findings, we propose that niche evolution, range dynamics, and their coupling shape the distribution of species, which provides insight into the eco-evolutionary processes that formed the current distribution of species in theC. zawadskiicomplex.

Ecological divergence of cryptic species of the atyid freshwater shrimps: Caridina indistincta and Paratya australiensis species complexes at different spatial scales in South-East Queensland, Australia

Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.

Cyperaceae in a data‐rich era: New evolutionary insights from solid frameworks

BackgroundSignificant shifts in climate are considered a threat to plants and animals with significant physiological limitations and limited dispersal abilities. The southern Appalachian Mountains are a global hotspot for plethodontid salamander diversity. Plethodontids are lungless ectotherms, so their ecology is strongly governed by temperature and precipitation. Many plethodontid species in southern Appalachia exist in high elevation habitats that may be at or near their thermal maxima, and may also have limited dispersal abilities across warmer valley bottoms.Methodology/Principal FindingsWe used a maximum-entropy approach (program Maxent) to model the suitable climatic habitat of 41 plethodontid salamander species inhabiting the Appalachian Highlands region (33 individual species and eight species included within two species complexes). We evaluated the relative change in suitable climatic habitat for these species in the Appalachian Highlands from the current climate to the years 2020, 2050, and 2080, using both the HADCM3 and the CGCM3 models, each under low and high CO2 scenarios, and using two-model thresholds levels (relative suitability thresholds for determining suitable/unsuitable range), for a total of 8 scenarios per species.Conclusion/SignificanceWhile models differed slightly, every scenario projected significant declines in suitable habitat within the Appalachian Highlands as early as 2020. Species with more southern ranges and with smaller ranges had larger projected habitat loss. Despite significant differences in projected precipitation changes to the region, projections did not differ significantly between global circulation models. CO2 emissions scenario and model threshold had small effects on projected habitat loss by 2020, but did not affect longer-term projections. Results of this study indicate that choice of model threshold and CO2 emissions scenario affect short-term projected shifts in climatic distributions of species; however, these factors and choice of global circulation model have relatively small affects on what is significant projected loss of habitat for many salamander species that currently occupy the Appalachian Highlands.

DEVELOPMENT OF SOIL AND LITTER ARTHROPOD ASSEMBLAGES IN RAINFOREST RESTORATION

High genetic diversity in the hydroid Plumularia setacea: A multitude of cryptic species or extensive population subdivision?

Identification of Fusarium isolates in a sample at the species level is an important and difficult task because many Fusarium species have similar morphological characteristics. The phylogenetic relations of species have been applied in Fusarium systematic and may solve taxonomic difficulties. The aim of the present study is to characterize pathogeny of Fusarium isolates through morphological analysis (concept of morphological species) associated with symptoms in hosts together with phylogeny analysis (concept of phylogenetic species) using internal transcribed spacer region (ITS) of ribosomal DNA for species identification. For the morphological characterization, Fusarium isolates were grown in PDA culture medium. Then, they were classified based on colony color and the microconidial, macroconidial and chlamydospore structures. The isolates were characterized molecularly by amplifying and sequencing the ITS region of the ribosomal DNA. The sequences generated were compared with those placed in the Genbank and Maximum Likelihood phylogenetic trees were constructed. Out of 14 isolates characterized morphologically and molecularly, five isolates were grouped in the Gibberella fujikuroi species complex in the Liseola section, seven presented characteristics of species from the Elegans section within the F. oxysporum species complex and two isolates presented characteristics of the section Gibbosum species complex in the F. incarnatum-equiseti species complex. Thus, seven isolates (section Elegans) belonged to the species F. oxysporum, two isolates (section Gibbosum) to the species F. equiseti. However, the ITS region of the ribosomal DNA did not provide sufficient evidence to define the species of G. fujikuroi species

Fusarium species are emerging pathogens known to cause both superficial and disseminated human infections. Aerosolized Fusarium species in healthcare settings have been associated with nosocomial fusariosis, particularly in patients with severe immunosuppression. To analyse the phylogenetic relationships of clinical and hospital environmental Fusarium isolates and assess their susceptibility to available antifungal agents. Clinical Fusarium isolates were procured from four hospitals in Taiwan, with environmental air and water sampling collected at Kaohsiung Chang Gung Memorial Hospital (KCGMH). All clinical and hospital environmental Fusarium isolates were identified through gene sequencing of translation elongation factor 1-α and internal transcribed spacer regions of ribosomal DNA. Antifungal susceptibility testing followed the CLSI M38-A3 broth microdilution method. A total of 41 clinical and 4 hospital environmental Fusarium isolates were identified, belonging to five species complexes (SC): F. solani SC (FSSC) (62.8%), F. fujikuroi SC (FFSC) (14.0%), F. incarnatum-equiseti SC (11.6%), F. dimerum SC (7.0%), and F. oxysporum SC (4.7%). Phylogenetic analysis revealed that clinical Fusarium isolates from KCGMH were closely related to environmental Fusarium isolates from air samples at the same hospital. Amphotericin B exhibited high activity against most Fusarium species. With the exception of FFSC, other Fusarium SC demonstrated significantly elevated MIC values to itraconazole, voriconazole, posaconazole, and isavuconazole. FSSC was the most prevalent SC in Taiwan, exhibiting higher MIC values for azoles than FFSC isolates. The clinical Fusarium isolates were observed to form clusters with the corresponding environmental isolates. The potential of airborne nosocomial infections in the healthcare environment cannot be overlooked.

Most of gall-inducers are monophagus or oligophagus, which utilize a narrow spectrum of host plants and organs. Diversity of gall inducers and the specific relationship between galling insects and host plants are considered as a consequence of adaptive radiation. Galls could be considered as extension of phenotypes of the gall indusers. This study focused on the relationship between Daphnephila spp. (Diptera: Cecidomyiidae) and Machilus (Lauraceae) in Taiwan based on morphological characters of insect and galls, molecular, and biological data in order to clarify the galler taxonomy and the phylogenetic relationship. After examining all the plant species of Machilus in Taiwan, the acquired galls were sorted into 38 morphological species based on their gall shape, galling position, and host plant information. Galls with similar shaped could be further groups into 8 series, i.e., spindle-shaped, needle-like, urn-shaped, little urn-shaped, obovate, club-shaped, bird-head-shaped and ovoid gall serieses. There are significant differences among gall seires but smaller variation within each gall series. Molecular analansis based on gene revealed that most of gall midges with similar shapes (gall morphospecies) are monophyletic group. Clear differentiation ranging from 1.3% to 14.3% exists between each group and only a few less than 2% which is mainly belong to club-shaped series. Morphological differences were found between midges from stem and leaf galls, espcieally on larval spatula and adult genitalia. Only trievial differences could be found for the midges within stem or leaf galling groups. The overall evdiences suggest that there are at least 9 species in Daphnephila, including 5 named species (Daphnephila sueyenae, D. ornithocephaia, D. stenocalia, D. taiwanensis, D. truncicola), and 4 new species. The stem gall midges inculed 1 named species (D. truncicola) and 3 unnamed species. The taxonomy of leaf gall midges are more complicated. The mouse-like gall series is a species complex, which contain D. taiwanensis and a cryptic species. The club-shaped, bird-head-like, and the urned-shaped series formed another species complex, including two named species (D. stenocalia and D. ornithocephala) and a new species (urned-shaped gall inducer). The midges of little urn-shaped gall series are the same species of midges belonging to obovate gall series (D. sueyenae). Field observation on midges indicates the clear synchronization between reproduction of adults and phenology of host plants. Females may secrete pheromone to mate with males and the galling position and patter are determined by females. To sum up, the gall shape series (except for little urn-shaped gall series) reflect the taxonomic status at species category of Daphnephila gall midges, whetheras the variability with gall shape series may not always reflect the species status. It is necessary to obtain eveidences from differet aspects and to integrate the overall variation for making correct taxonomic determination for the gall midges.

Silas Bossert, Barbara-Amina Gereben-Krenn, Johann Neumayer, Bernhard Schneller, and Harald W. Krenn (2016) The Bombus lucorum complex represents a group of three distinct but cryptic bumblebee species in Europe. With the advent of DNA-based identification methods, their species status was confirmed and the use of COI barcoding proved to be an especially useful tool for species identification within the group. Meanwhile, the identification based on morphology remains difficult and recent studies challenged the general distinguishability by revealing an important character to be unreliable. This has consequences for our understanding of the distribution and ecology of the species in Europe and aggravates our patchy knowledge of the situation in Austria and the whole area of the European Alps. In this study, we investigate the exact species composition and distribution of the Bombus lucorum complex in Austria based on the reliable species identification with COI sequence data. The habitat usage is studied and the first extensive investigation of altitudinal and climatic differentiation is provided. The results support three distinct genotypic groups in the Bombus lucorum complex. B. lucorum and B. cryptarum co-occur in several areas across the country, with B. lucorum being the most common and most widespread species. The study provides no evidence for the presence of B. magnus in Austria. The less common species, B. cryptarum, mainly occurs in the high mountains and is the predominant species of the complex above altitudes of 2100 m a.s.l. Further, B. cryptarum is almost absent from woodlands and is relatively more abundant in habitats with colder climate than B. lucorum in Austria. Additionally, the results indicate a very low intraspecific genetic variation within B. lucorum and B. cryptarum. This study confirms previous findings of three distinct species within the species complex. Based on reliable COI identification, the first coherent overview of the species complex in Austria can be achieved. The climatic data allows us to explain the differences in the distribution patterns. Moreover, the low intraspecific variation may indicate past bottleneck conditions for B. lucorum and B. cryptarum.

Systematics of the golden trapdoor spiders (Araneae: Idiopidae: Euoplini) of eastern Australia

Cryptic species complexes are common among parasites, which tend to have large populations and are subject to rapid evolution. Such complexes may arise through host-parasite co-evolution and/or host switching. For parasites that reproduce directly on their host, there might be increased opportunities for sympatric speciation, either by exploiting different hosts or different micro-habitats within the same host. The genus Gyrodactylus is a specious group of viviparous monogeneans. These ectoparasites transfer between teleosts during social contact and cause significant host mortality. Their impact on the guppy (Poecilia reticulata), an iconic evolutionary and ecological model species, is well established and yet the population genetics and phylogenetics of these parasites remains understudied. Using mtDNA sequencing of the host and its parasites, we provide evidence of cryptic speciation in Gyrodactylus bullatarudis, G. poeciliae and G. turnbulli. For the COII gene, genetic divergence of lineages within each parasite species ranged between 5.7 and 17.2%, which is typical of the divergence observed between described species in this genus. Different lineages of G. turnbulli and G. poeciliae appear geographically isolated, which could imply allopatric speciation. In addition, for G. poeciliae, co-evolution with a different host species cannot be discarded due to its host range. This parasite was originally described on P. caucana, but for the first time here it is also recorded on the guppy. The two cryptic lineages of G. bullatarudis showed considerable geographic overlap. G. bullatarudis has a known wide host range and it can also utilize a killifish (Anablepsoides hartii) as a temporary host. This killifish is capable of migrating overland and it could act as a transmission vector between otherwise isolated populations. Additional genetic markers are needed to confirm the presence of these cryptic Gyrodactylus species complexes, potentially leading to more in-depth genetic, ecological and evolutionary analyses on this multi-host-parasite system.

AimIn geographically and ecologically heterogeneous landscapes, such as tropical mountains, widely distributed species may be informative proxies for studying landscape and climatic evolution. We explore historical vicariant and dispersal processes that may have determined the genetic structure and variation of a palm species complex living in cloud forests. We hypothesize that the genomic groupings reflect uplift‐based isolation by vicariance, divergence via dispersal events driven by faulted montane segments or recent divergence due to climate fluctuations.LocationColombian Andes.TaxonGeonoma undata–G. orbignyana species complex (Arecaceae).MethodsWe sampled 195 individuals of the species complex plus the outgroup (G. interrupta) across the three cordilleras of Colombia, the Colombian Massif and the Sierra Nevada de Santa Marta. We used target capture sequencing to generate a dataset of 12,750 quality‐filtered genome‐wide SNPs. We conducted phylogenetic, multivariate and population genomics and structure analyses to infer demographical history.ResultsWe found four genetically distinct groups within the species complex. The geographical distributions of the genetic groups, and their inferred phylogenetic and population divergence are consistent with a history of colonization of mountain segments that were disconnected until the late Pliocene. These breaks coincide with the distribution of Pliocene strike‐slip faulting events.Main conclusionsThe faulting and resultant topographic disruption of the northernmost Andean cordillera prior to the onset of the Pleistocene is implied by the presence of phylogeographic breaks in areas that are topographically continuous today. These cordilleras were formed by connecting segments that were previously uplifted but historically detached in areas where dense fault systems occur. Large‐scale strike‐slip faulting can generate topographic gaps, features that likely caused the divergence by dispersal with gene flow of the Geonoma undata–G. orbignyana complex.

Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex. The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.