Phylogenetics and Population Genetics of the Petrolisthes lamarckii-P. haswelli Complex in China: Old Lineage and New Species

Petrolisthes lamarckii (Leach, 1821) and P. haswelli Miers, 1884 are a pair of sister species of porcelain crabs, both of which are common in the intertidal zone of southern China, typically found under rocks and in the crevices of coral reefs. However, the distribution, genetic relationship and diversity of the two species in China have not been rigorously studied. Meanwhile, P. lamarckii is considered as a complex of cryptic species due to their diverse morphological features. In this study, we identified 127 specimens of the P. lamarckii-P. haswelli complex (LH complex) and recognised a new species through morphological and molecular analysis. Furthermore, we constructed a time-calibrated phylogeny of the LH complex using three mitochondrial and two nuclear genes from all three species, finding that the divergence of the LH complex can be traced back to the Miocene epoch, and that the genetic diversity increased during the Mid-Pleistocene transition period. Glacial refugia formed during the Pleistocene climatic oscillations has been regarded as one of the contributing factors to the diversification of marine organisms in the north-western Pacific. Petrolisthes haswelli demonstrates a wide distribution along the southern coast of China, while other lineages display more restricted distributions. The research on the demographic history and gene flow of P. haswelli revealed that the Chinese coastal populations experienced an expansion event approximately 12.5 thousand years ago (Kya) and the asymmetrical gene flows were observed between the two sides of the Taiwan Strait and Qiongzhou Strait, respectively, which is likely influenced by the restriction of ocean currents.

An integrative taxonomic review of the Natal mountain catfish, Amphilius natalensis Boulenger 1917 (Siluriformes, Amphiliidae), with description of four new species

An integrative taxonomic analysis combining mitochondrial cytochrome oxidase subunit I sequences, morphology, colour pattern and two species delimitation approaches revealed the existence of five lineages within the Natal mountain catfish, Amphilius natalensis, in southern Africa. These lineages are separated by substantial genetic divergences (1.6%-9.46%), and they can be consistently distinguished from one another based on a combination of morphology and colour pattern differences. Additionally, the lineages are allopatrically distributed and confined to isolated river systems draining discrete mountain ranges, which makes gene flow among them unlikely. One of these lineages is A. natalensis s.s., which is confined to the uMngeni and Tukela river systems in KwaZulu Natal (KZN) Province in South Africa. The other four lineages represent new species to science which are described as Amphilius zuluorum sp. nov., endemic to the uMkhomazi River system in KZN, Amphilius engelbrechti sp. nov., endemic to the Inkomati River system in Mpumalanga Province in South Africa, Amphilius marshalli sp. nov., endemic to the Pungwe and Lower Zambezi river systems in Zimbabwe and Mozambique, and Amphilius leopardus sp. nov., endemic to the Ruo River in Malawi. The results show that Amphilius laticaudatus which is endemic to the Buzi River system in Zimbabwe and Mozambique, belongs to the A. natalensis s.l. complex. A redescription of A. laticaudatus is presented and an updated identification key for the mountain catfishes of southern Africa is provided.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Integrated analysis of the ringneck snake Diadophis punctatus complex (Colubridae: Dipsadidae) in a biodiversity hotspot provides the foundation for conservation reassessment

Species classification may not reflect the underlying/cryptic genetic diversity and focusing on groups that do not represent historically independent units can misdirect conservation efforts. The identification of evolutionarily significant units (ESUs) allows cryptic genetic diversity to be accounted for when designating conservation priorities. We used multi-locus coalescent-based species delimitation methods and multivariate analyses of morphological data to examine whether the subspecies merit conservation recognition and infer the ESUs in ringneck snakes (Diadophis punctatus) throughout the California Floristic Province. Species delimitation methods failed to recover groups consistent with designated subspecies and instead inferred three well supported, mostly geographically isolated lineages. Divergence time estimates suggest that the divergences were driven by historical isolation associated with Pleistocene climate shifts. We found a correlation between increased morphological differentiation and time since divergence, and greater niche similarity between the more recently diverged eastern California and western California groups. Based on these results, we propose that the morphological similarities are due to a combination of morphological conservatism and evolutionary stasis. Our study provides the foundation necessary to re-assess the biodiversity and conservation status of ringneck snakes and offers an important step in unveiling the diversity within the western portion of the genus’ range.

Integrative taxonomy reveals hidden diversity in the southern African darters genus Nannocharax Günther 1867 (Characiformes: Distichodontidae)

The present study explored the diversity of Nannocharax within southern Africa by implementing three species delimitation methods for a data set consisting of 37 mitochondrial cytochrome oxidase subunit I sequences. Two unilocus coalescent methods, the General Mixed Yule Coalescent (GMYC) and the Bayesian implementation of the Poisson Tree Processes (bPTP), and a genetic distance method, the Automatic Barcode Gap Discovery (ABGD), were applied. Both GMYC and bPTP delimited the same operational taxonomic units (OTUs), revealing a higher diversity for the genus in the region than previously recognised, whereas the ABGD failed to delimit the same candidate species. All methods delimited two species groups, and these are supported based on colouration patterning and morphology; the Nannocharax multifasciatus and the Nannocharax macropterus species groups and the delimited OTUs were assigned to each. Two putative new species were identified, Nannocharax cf. lineostriatus "Okavango" from the Okavango River in Angola and N. cf. lineostriatus "Kwanza" from the Kwanza River system in Angola. The distribution of Nannocharax dageti was confirmed for the Upper Zambezi and extended to the Okavango system, and an identification key for the southern Africa Nannocharax species is provided.

Geographical isolation and restricted gene flow drive speciation of Aegla singularis (Decapoda: Anomura: Aeglidae) in southern South America

Geographical isolation is a key element in allopatric speciation. If gene flow is interrupted for long enough by geographical barriers, populations can evolve independently and eventually form distinct species. Aegla singularis provides an ideal model to study this process due to the characteristics of the geographical area that it occupies and its limited dispersal ability. Aegla singularis inhabits streams of the Uruguay and Paraná River basins in the Neotropical region of South America. The basins are separated by the Sierra Central Mountains. Here we studied the speciation of A. singularis resulting from geographical isolation by using molecular and morphometric data. Individuals of A. singularis were analysed using geometric morphometrics and genetic data (COII and EFα1). We found significant differences in shape and genetics between A. singularis populations from the two basins. These differences suggest ongoing divergence due to restricted gene flow caused by the geographical barrier of the Sierra Central Mountains, indicating that the populations of the Parana and Uruguay River slopes are undergoing divergence.

Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae)

The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.

Does the landscape surrounding streams affect the occurrence of freshwater crabs? A case study of the genus Aegla (Crustacea: Decapoda: Anomura) in subtropical basins

ABSTRACT Changes in the landscape where watersheds are located may affect the stream biota in different ways. In order to explore this idea, we collected freshwater crabs of the genus Aegla Leach, 1820 in subtropical region of southern Brazil. We also measured a number of landscape features and physico-chemical variables in the collection streams and surroundings in order to ascertain which factors affect the occurrence of these crustaceans. A total of 167 individuals of Aegla were collected in 21 streams. The collection was comprised of three species: A. odebrechtii, A. platensis, and A. singularis. The occurrence of A. platensis was influenced by physico-chemical variables (total carbon and total organic carbon) and stream morphometry factors (level curves sum). The occurrence of A. singularis was influenced by land use (pasture and exposed soil and agriculture) and the stream morphometry (level curves sum). Only a small number of A. odebrechtii were collected and their occurrence was influenced by land use (pasture and exposed soil and agriculture). The topography of the area studied limits the types of land use and areas that are less favorable for agriculture (more hilly areas) are have more riparian vegetation (or less anthropic stress). As a result, these areas are less subject to changes in water quality, which is reflected in the distribution of Aegla species.

Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion

Stream fishes of the Eastern Afromontane region are among the least studied vertebrates in this region, despite the potential for harbouring cryptic diversity. The present study examined mitochondrial cytochrome oxidase subunit I (COI) sequence divergence in 153 specimens of stream fishes belonging to four genera and three families, [(Amphilius and Zaireichthys (Amphiliidae); Chiloglanis (Mochokidae); and Hippopotamyrus (Mormyridae)], in the Eastern Zimbabwe Highlands (EZH) freshwater ecoregion to explore the extent to which the current taxonomy conceals the ichthyofaunal diversity in the region. The General Mixed Yule Coalescent (GMYC) species delineation method identified 14 clusters within five currently recognised ‘species’ from the EZH ecoregion. Only one of these clusters represents a named species, while 13 of them represent candidate or undescribed species. Our results revealed that effective conservation of this region’s unique biota is limited by the incomplete knowledge of taxonomic diversity and inaccurate mapping of species distribution ranges.