Cryptic diversity in the Western Balkan endemic copepod: Four species in one?

Wastewater and warming effects on aquatic invertebrates: Experimental insights into multi-level biodiversity consequences

Wastewater effluents and global warming affect freshwater ecosystems and impact their crucial biodiversity. Our study aimed at characterizing individual and combined impacts of wastewater effluent and increased water temperature (as one aspect of climate change) on model freshwater communities. We tested the effect of experimental treatments on genetic diversity, survival, body weight, total lipid content, lipidome and metabolome of individual species as well as community composition and phylogenetic diversity. In a 21-day mesocosm experiment we assessed the responses of a simplified freshwater food web comprising of moss and seven species of benthic macroinvertebrate shredders and grazers (mayflies, stoneflies, caddisflies and amphipods) to four treatments in a full factorial design: control, increased water temperature, wastewater and a multiple stressor treatment combining increased temperature and wastewater. Physiological responses varied among taxa, with species-specific sensitivities observed in survival and lipid content. The lowest total lipid content was observed in caddisflies and a mayfly subjected to multiple stressor treatment. The effects of stressors were reflected in the altered metabolic pathways and lipid metabolism of the individual taxa, with differential treatment effects also observed between taxa. A notable decrease in phylogenetic diversity was observed across all experimental communities. Gammarus fossarum demonstrated a high susceptibility to environmental stressors at the genetic level. Hence, while commonly used indicators of ecosystem health (e.g. community composition) remained stable, molecular indicators (e.g. phylogenetic diversity, metabolome and lipidome) responded readily to experimental treatments. These findings underscore the vulnerability of macroinvertebrates to environmental stressors, even over relatively short exposure periods. They highlight the importance of molecular indicators in detecting immediate ecological impacts, offering valuable information for conservation strategies and understanding the ecological consequences in freshwater ecosystems.

Cryptic diversity and speciation in an endemic copepod crustacean Harpacticella inopinata within Lake Baikal

Ancient lakes are hotspots of species diversity, posing challenges and opportunities for exploration of the dynamics of endemic diversification. Lake Baikal in Siberia, the oldest lake in the world, hosts a particularly rich crustacean fauna, including the largest known species flock of harpacticoid copepods with some 70 species. Here, we focused on exploring the diversity and evolution within a single nominal species, Harpacticella inopinata Sars, 1908, using molecular markers (mitochondrial COI, nuclear ITS1 and 28S rRNA) and a set of qualitative and quantitative morphological traits. Five major mitochondrial lineages were recognized, with model-corrected COI distances of 0.20-0.37. A concordant pattern was seen in the nuclear data set, and qualitative morphological traits also distinguish a part of the lineages. All this suggests the presence of several hitherto unrecognized cryptic taxa within the baikalian H. inopinata, with long independent histories. The abundances, distributions and inferred demographic histories were different among taxa. Two taxa, H. inopinata CE and H. inopinata CW, were widespread on the eastern and western coasts, respectively, and were largely allopatric. Patterns in mitochondrial variation, that is, shallow star-like haplotype networks, suggest these taxa have spread through the lake relatively recently. Three other taxa, H. inopinata RE, RW and RW2, instead were rare and had more localized distributions on either coast, but showed deeper intraspecies genealogies, suggesting older regional presence. The rare taxa were often found in sympatry with the others and occasionally introgressed by mtDNA from the common ones. The mitochondrial divergence between and within the H. inopinata lineages is still unexpectedly deep, suggesting an unusually high molecular rate. The recognition of true systematic diversity in the evaluation and management of ecosystems is important in hotspots, as it is everywhere else, while the translation of the diversity into a formal taxonomy remains a challenge.

Genetic Variability of Polypedilum (Diptera: Chironomidae) from Southwest Ecuador

Simple Summary

Polypedilum is a genus of aquatic non-biting midges in the family Chironomidae. This genus is widely distributed in neotropical rivers from lowlands to Andean highlands. Nevertheless, making species identification based on morphology is quite complex, even more so in the Neotropics, since systematic studies of this group are scarce. DNA barcoding can help to overcome this problem using a short DNA sequence as a barcode for species delimitation. A fragment of the mitochondrial gene cytochrome c oxidase I (CO1) has been successfully employed as a barcode in the genus Polypedilum. In this study, our aim was to understand the effect of environmental characteristics on Polypedilum diversity and distribution. We examined the CO1 sequence of 68 Polypedilum specimens from rivers with different environmental conditions located in an important biogeographic area of Ecuador. We identified five morphotypes and seven putative species which revealed high genetic variability among them. Polypedilum distribution seems to be affected mainly by two environmental factors, dissolved oxygen, and temperature. Our study is the first evidence of richness within the genus in Ecuador, highlighting the importance of developing taxonomic studies along with ecological assessments to further describe and identify new species.

Abstract

Chironomids show a wide distribution and can occupy several habitats due to their high adaptive capacity in different freshwater environments. The genus Polypedilum is found along a wide elevational and environmental gradient in the neotropics, and its genetic variability could help to elucidate factors determining its distribution and tolerance to the environmental changes of different species or populations. This study examines the genetic variability of Polypedilum in an important biogeographic area that acts as a geographical barrier of biodiversity at the border of the Choco and Tumbes biomes. We identified five Polypedilum morphotypes using classic taxonomic methods. We examined 68 Polypedilum individuals from eight sampling sites in El Oro Province, Ecuador, analyzing the putative molecular species using the cytochrome c oxidase subunit 1 (CO1) mitochondrial gene fragment. Then, we calculated molecular diversity indices, Haplotype diversity (Hd), and θs and θπ estimators. Seven Polypedilum OTUs were determined from which a high molecular diversity was registered. A CCA was conducted to understand the population composition in relation to environmental characteristics. Results indicated that dissolved oxygen and temperature are the main environmental factors affecting Polypedilum distribution across elevational gradients and between basins.

Morphological and molecular diversity patterns of the genus Tropodiaptomus Kiefer, 1932 (Copepoda, Calanoida, Diaptomidae) in Thailand

Tropodiaptomus is one of the most specious genera in the family Diaptomidae, but it is often rare in terms of distribution and abundance. Moreover, Tropodiaptomus species show a noteworthy variability in some of the morphological characters considered of prime importance in diaptomid taxonomy, and the presence of cryptic or pseudocryptic species is likely. Thus, through a geographically-wide sampling in Thailand, we aimed to investigate the local diversity of the genus and to compare the morphological and molecular diversity pattern based on mitochondrial and nuclear genes sequences. DNA taxonomy was also implemented in order to check whether the Tropodiaptomus lineages were independent species according to the “evolutionary genetic species concept”. Six Tropodiaptomus morphospecies were found, three of which are putative species new to Science pending a formal description. The finding of such a high incidence of undescribed species stresses the existence of a significant “Linnean shortfall” affecting Thai diaptomids. The molecular results showed that most of the studied species could be identified consistently with their morphology-based taxonomy. However, Tropodiaptomus vicinus and T. cf. lanaonus showed a high level of genetic diversity, suggesting that traditional morphological techniques might be inadequate for correctly assessing their taxonomical status.

Geographic Variation of Phyllodiaptomus tunguidus Mitogenomes: Genetic Differentiation and Phylogeny

Phyllodiaptomus tunguidus (Copepoda: Calanoida) is largely endemic to and widespread in freshwater in southern China, where it inhabits a complex landscape from lowland to highland across an elevation gradient of 2000m. A deep genetic differentiation can be expected between its most distant geographic populations. Here, we sequenced nine mitogenomes from diverse populations. All mitogenomes contained 37 genes, including 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes and one control region. Their base composition, genetic distance and tRNA structure indeed revealed a wide differentiation between mitogenomes. Two P. tunguidus from Guangxi near Vietnam differed from the other seven by up to 10.1%. Their tRNA-Arg had a complete clover-leaf structure, whereas that of the others did not contain an entire dihydrouridine arm. The nine mitogenomes also differed in the length of rRNA. NJ, ML, and Bayesian analyses all split them into two clades, viz. the two P. tunguidus from Guangxi (Clade 1), and the other seven (Clade 2). Both the structure and phylogeny of the mitogenomes suggest that P. tunguidus has complex geographic origin, and its populations in Clade 1 have long lived in isolation from those in Clade 2. They currently reach the level of subspecies or cryptic species. An extensive phylogenetic analysis of Copepoda further verified that Diaptomidae is the most recently diverging family in Calanoida and that P. tunguidus is at the evolutionary apex of the family.

Phylogeography and genetic diversity of the copepod family Cyclopidae (Crustacea: Cyclopoida) from freshwater ecosystems of Southeast Nigeria

Background

Copepods are key components of aquatic ecosystems and can help regulate the global carbon cycle. Much attention has been paid to the species diversity of copepods worldwide, but the phylogeography and genetic diversity of copepods in Nigeria is unexplored.

Results

Using a mitochondrial cytochrome c oxidase subunit I marker, we preformed phylogenetic and phylogeographic analyses for Cyclopidae copepods in Southeast Nigeria. A high species diversity of Cyclopidae in Nigeria: 5 species of Tropocyclops, 5 species of Mesocyclops and 2 species of Thermocyclops from Cyclopidae were identified in 15 populations. Moreover, we detected 18 unique haplotypes, which fell into two distinct clades. Pairwise genetic distances (uncorrected p-distances) among the species of Cyclopidae ranged from 0.05 to 0.257. Several species co-existed in the same lake, and some haplotypes were shared among different geographic populations, suggesting a dispersal of Cyclopidae in our sampling region. Finally, we found that the population genetic diversity for each species of Cyclopidae was low in Nigeria.

Conclusions

Our findings explored the species diversity and distribution of copepods within the family Cyclopidae for 15 Nigerian freshwater ecosystems: a high species diversity of Cyclopidae copepods was detected over a small geographic sampling range. Results from this study contribute to a better understanding of copepod diversity of Nigerian freshwater ecosystems.

Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific

Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorly known Southeast Pacific region, with samples spanning an ocean gradient from coastal upwelling to the oligotrophic South Pacific Subtropical Gyre. We assessed variation in fragments of the mitochondrial (mt) genes cytochrome c oxidase subunit I (COI) and Cytochrome b as well as in the nuclear internal transcribed spacer (ITS) region and 28 S rRNA. Phylogenetic analyses revealed the presence of 8 divergent lineages occurring across the gradient with genetic distances in the range of 0.036 and 0.44 (mt genes), and GMYC species delimitation methods support their inference as distinct (undescribed) species. Genetic lineages occurring across the zonal gradient showed strong genetic structuring, with the presence of at least two new lineages within the coastal upwelling zone, revealing an unexpectedly high level of endemism within the Humboldt Current System. Multivariate analyses found strong correlation between genetic variation and surface chlorophyll-a and salinity, suggesting an important role for hydrographic gradients in maintaining genetic diversity. However, the presence of cryptic lineages within the upwelling zone cannot be easily accounted for by environmental heterogeneity and poses challenging questions for understanding the speciation process for oceanic zooplankton.

Transcriptome analysis of two radiated Cycas species and the subsequent species delimitation of the Cycas taiwaniana complex

PREMISE

Cycas is an important gymnosperm genus, and the most diverse of all cycad genera. The C. taiwaniana complex of species are morphologically similar and difficult to distinguish due to a lack of genomic resources.

METHODS

We characterized the transcriptomes of two closely related and endangered Cycas species endemic to Hainan, China: C. hainanensis and C. changjiangensis. Three single-copy nuclear genes in the C. taiwaniana complex were sequenced based on these transcriptomes, enabling us to evaluate the species boundaries using the multispecies coalescent method implemented in the Bayesian Phylogenetics and Phylogeography program.

RESULTS

We obtained 68,184 and 81,561 unigenes for C. changjiangensis and C. hainanensis, respectively. We identified six positively selected genes that are mainly involved in stimulus responses, suggesting that environmental adaptation may have played an important role in the relatively recent divergence of these species. The similar K S distribution peaks at 1.0 observed for the paralogs in the two species indicate a common whole-genome duplication event. Our species delimitation analysis indicated that the C. taiwaniana complex consists of three distinct species, which correspond to the previously reported morphological differences.

DISCUSSION

Our study provides valuable genetic resources for Cycas species and guidance for the taxonomic treatment of the C. taiwaniana complex, as well as new insights into evolution of species within Cycas.

Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios

Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use of molecular approaches for species delimitation. Among the most widely used methods, the generalized mixed Yule-coalescent (GMYC) and Poisson tree processes (PTP) were designed for the analysis of single-locus data but are often applied to concatenations of multilocus data. In contrast, the Bayesian multispecies coalescent approach in the software Bayesian Phylogenetics and Phylogeography (BPP) explicitly models the evolution of multilocus data. In this study, we compare the performance of GMYC, PTP, and BPP using synthetic data generated by simulation under various speciation scenarios. We show that in the absence of gene flow, the main factor influencing the performance of these methods is the ratio of population size to divergence time, while number of loci and sample size per species have smaller effects. Given appropriate priors and correct guide trees, BPP shows lower rates of species overestimation and underestimation, and is generally robust to various potential confounding factors except high levels of gene flow. The single-threshold GMYC and the best strategy that we identified in PTP generally perform well for scenarios involving more than a single putative species when gene flow is absent, but PTP outperforms GMYC when fewer species are involved. Both methods are more sensitive than BPP to the effects of gene flow and potential confounding factors. Case studies of bears and bees further validate some of the findings from our simulation study, and reveal the importance of using an informed starting point for molecular species delimitation. Our results highlight the key factors affecting the performance of molecular species delimitation, with potential benefits for using these methods within an integrative taxonomic framework.

Karyosystematics and molecular taxonomy of the anomalous blue butterflies (Lepidoptera, Lycaenidae) from the Balkan Peninsula

The Balkan Peninsula represents one of the hottest biodiversity spots in Europe. However, the invertebrate fauna of this region is still insufficiently investigated, even in respect of such well-studied organisms as Lepidoptera. Here we use a combination of chromosomal, molecular and morphological markers to rearrange the group of so-called anomalous blue butterflies (also known as 'brown complex' of the subgenus Agrodiaetus Hübner, [1822] and as the Polyommatus (Agrodiaetus) admetus (Esper, 1783) species group) and to reveal its cryptic taxonomic structure. We demonstrate that Polyommatus aroaniensis (Brown, 1976) is not as widespread in the Balkans as was previously thought. In fact, it has a dot-like distribution range restricted to the Peloponnese Peninsula in South Greece. Polyommatus orphicus Kolev, 2005 is not as closely related to the Turkish species Polyommatus dantchenkoi (Lukhtanov & Wiemers, 2003) as was supposed earlier. Instead, it is a Balkan endemic represented by two subspecies: Polyommatus orphicus orphicus (Bulgaria) and Polyommatus orphicus eleniae Coutsis & De Prins, 2005 (Northern Greece). Polyommatus ripartii (Freyer, 1830) is represented in the Balkans by an endemic subspecies Polyommatus ripartii pelopi. The traditionally recognized Polyommatus admetus (Esper, 1783) is shown to be a heterogeneous complex and is divided into Polyommatus admetus sensu stricto (the Balkans and west Turkey) and Polyommatus yeranyani (Dantchenko & Lukhtanov, 2005) (east Turkey, Armenia, Azerbaijan and Iran). Polyommatus nephohiptamenos (Brown & Coutsis, 1978) is confirmed to be a species with a dot-like distribution range in Northern Greece. Finally, from Central Greece (Timfristos and Parnassos mountains) we describe Polyommatus timfristos Lukhtanov, Vishnevskaya & Shapoval, sp. n. which differs by its haploid chromosome number (n=38) from the closely related and morphologically similar Polyommatus aroaniensis (n=47-48) and Polyommatus orphicus (n=41-42). We provide chromosomal evidence for three separate south Balkan Pleistocene refugia (Peloponnesse, Central Greece and Northern Greece/South Bulgaria) and stress the biogeographic importance of Central Greece as a place of diversification. Then we argue that the data obtained have direct implications for butterfly karyology, taxonomy, biogeography and conservation.