The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan

An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.

Deep Genotypic Species Delimitation of Aspergillus Section Flavi Isolated from Brazilian Foodstuffs and the Description of Aspergillus annui sp. nov. and Aspergillus saccharicola sp. nov

Aspergillus section Flavi is a fungal group that is important in food because it contains spoilage and potentially aflatoxigenic species. Aflatoxins are metabolites that are harmful to human and animal health and have been recognized as the primary natural contaminant in food. Therefore, recognizing the biodiversity of this group in food is necessary to reduce risks to public health. Our study aimed to investigate the diversity of Aspergillus section Flavi isolated from Brazilian foodstuffs such as cassava, sugarcane, black pepper, paprika, Brazil nuts, yerba-mate, peanuts, rice, and corn. A polyphasic approach integrating phenotypic data and multilocus genotypic analyses (CaM, BenA, and RPB2) was performed for 396 strains. Two new species in the Aspergillus subgenus Circumdati section Flavi are proposed using maximum-likelihood analysis, Bayesian inference, and coalescence-based methods: Aspergillus saccharicola sp. nov. and Aspergillus annui sp. nov. A. saccharicola sp. nov. belongs to the series Flavi, is a potentially aflatoxigenic species (B1, B2, G1, and G2), closely related to Aspergillus arachidicola, and was found mostly in sugarcane. A. annui sp. nov. was isolated from samples of sweet paprika. To accommodate A. annui sp. nov., a new series Annuorum was proposed.

Phylogeny and Cryptic Diversity of Diopatra (Onuphidae, Annelida) in the East Atlantic

Diopatra Audouin & Milne-Edwards, 1833 is a species rich genus that is common in tropical and subtropical regions. The genus is readily identified by its striking, spiral branchiae, but species identification has historically been challenging due to a high variation in diagnostic characters used. This study aims to reconstruct the phylogeny of Diopatra with molecular markers and assess the species diversity of West African Diopatra with the species delimitation programs bPTP and BPP. Specimens were collected from Morocco to Angola, and the markers COI, 16S and 28S were sequenced from 76 specimens. The constructed phylogeny retrieved Diopatra as monophyletic, as well as five well supported clades within the genus. All clades were defined by morphological characters, some of which have previously not been considered to have high phylogenetic or taxonomical value. Species delimitation analyses recovered 17 new species, several of which were not readily identified morphologically. One species complex comprising between one and 12 species was left unresolved due to incongruence between the species delimitation methods and challenging morphology. Our results indicate that the diversity of Diopatra is significantly underestimated, where this regional study near to doubled the number ofknown species from the East Atlantic.

Plotting for change: an analytical framework to aid decisions on which lineages are candidate species in phylogenomic species discovery

A recent study argued that coalescent-based models of species delimitation mostly delineate population structure, not species, and called for the validation of candidate species using biological information additional to the genetic information, such as phenotypic or ecological data. Here, we introduce a framework to interrogate genomic datasets and coalescent-based species trees for the presence of candidate species in situations where additional biological data are unavailable, unobtainable or uninformative. For de novo genomic studies of species boundaries, we propose six steps: (1) visualize genetic affinities among individuals to identify both discrete and admixed genetic groups from first principles and to hold aside individuals involved in contemporary admixture for independent consideration; (2) apply phylogenetic techniques to identify lineages; (3) assess diagnosability of those lineages as potential candidate species; (4) interpret the diagnosable lineages in a geographical context (sympatry, parapatry, allopatry); (5) assess significance of difference or trends in the context of sampling intensity; and (6) adopt a holistic approach to available evidence to inform decisions on species status in the difficult cases of allopatry. We adopt this approach to distinguish candidate species from within-species lineages for a widespread species complex of Australian freshwater fishes (Retropinna spp.). Our framework addresses two cornerstone issues in systematics that are often not discussed explicitly in genomic species discovery: diagnosability and how to determine it, and what criteria should be used to decide whether diagnosable lineages are conspecific or represent different species.

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Cryptic species – genetically distinct species that are morphologically difficult to distinguish – present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole use of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean bark anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate species based on genetic data can be accurately diagnosed. We also test alternative species delimitation scenarios with a model fitting approach that evaluates normal mixture models capable of identifying morphological clusters. Our analyses reject the hypothesis that the candidate species are diagnosable. Neither uni- nor multivariate morphometric data distinguish candidate species. The best-supported model included two morphological clusters; however, these clusters were uneven and did not align with a plausible species divergence scenario. After removing two related traits driving this result, only one cluster was supported. Despite substantial differentiation revealed by genetic data, we recover no new evidence to delimit species and refrain from taxonomic revision. This study highlights the importance of considering other types of data along with molecular data when delimiting species.

The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.

Phylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest

The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.

Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex

Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages L_N , L_S and L_HN ) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with L_HN /L_S split at 1.33 Ma and L_N /(L_HN +L_S ) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between L_HN and L_S was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages L_N and (L_S +L_HN ) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: L_HN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; L_S represents a cryptic species distributed throughout the southern Chinese continent; and L_N represents the nominotypical species L. edwardsi.

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.

High cryptic species diversity is revealed by genome-wide polymorphisms in a wild relative of banana, Musa itinerans, and implications for its conservation in subtropical China

BACKGROUND

Species delimitation is a challenging but essential task in conservation biology. Morphologically similar species are sometimes difficult to recognize even after examination by experienced taxonomists. With the advent of molecular approaches in species delimitation, this hidden diversity has received much recent attention. In addition to DNA barcoding approaches, analytical tools based on the multi-species coalescence model (MSC) have been developed for species delimitation. Musa itinerans is widely distributed in subtropical Asia, and at least six varieties have been documented. However, the number of evolutionarily distinct lineages remains unknown.

RESULTS

Using genome resequencing data of five populations (making up four varieties), we examined genome-wide variation and found four varieties that were evolutionary significant units. A Bayesian Phylogenetics and Phylogeography (BP&P) analysis using 123 single copy nuclear genes support three speciation events of M. itinerans varieties with robust posterior speciation probabilities; However, a Bayes factor delimitation of species with genomic data (BFD*) analysis using 1201 unlinked single nucleotide polymorphisms gave decisive support for a five-lineage model. When reconciling divergence time estimates with a speciation time scale, a modified three-lineage model was consistent with that of BP&P, in which the speciation time of two varieties (M. itinerans var. itinerans and M. itinerans var. lechangensis) were dated to 26.2 kya and 10.7 kya, respectively. In contrast, other two varieties (M. itinerans var. chinensis and M. itinerans var. guangdongensis) diverged only 3.8 kya in the Anthropocene; this may be a consequence of genetic drift rather than a speciation event.

CONCLUSION

Our results showed that the M. itinerans species complex harbours high cryptic species diversity. We recommend that M. itinerans var. itinerans and M. itinerans var. lechangensis be elevated to subspecies status, and the extremely rare latter subspecies be given priority for conservation. We also recommend that the very recently diverged M. itinerans var. chinensis and M. itinerans var. guangdongensis should be merged under the subspecies M. itinerans var. chinensis. Finally, we speculate that species delimitation of recently diverged lineages may be more effective using genome-wide bi-allelic SNP markers with BFD* than by using unlinked loci and BP&P.

Gene flow and Andean uplift shape the diversification of Gasteracantha cancriformis (Araneae: Araneidae) in Northern South America

The Andean uplift has played a major role in shaping the current Neotropical biodiversity. However, in arthropods other than butterflies, little is known about how this geographic barrier has impacted species historical diversification. Here, we examined the phylogeography of the widespread color polymorphic spider Gasteracantha cancriformis to evaluate the effect of the northern Andean uplift on its divergence and assess whether its diversification occurred in the presence of gene flow. We inferred phylogenetic relationships and divergence times in G. cancriformis using mitochondrial and nuclear data from 105 individuals in northern South America. Genetic diversity, divergence, and population structure were quantified. We also compared multiple demographic scenarios for this species using a model-based approach (phrapl) to determine divergence with or without gene flow. At last, we evaluated the association between genetic variation and color polymorphism. Both nuclear and mitochondrial data supported two well-differentiated clades, which correspond to populations occurring on opposite sides of the Eastern cordillera of the Colombian Andes. The final uplift of this cordillera was identified as the most likely force that shaped the diversification of G. cancriformis in northern South America, resulting in a cis- and trans-Andean phylogeographic structure for the species. We also found shared genetic variation between the cis- and trans-Andean clades, which is better explained by a scenario of historical divergence in the face of gene flow. This has been likely facilitated by the presence of low-elevation passes across the Eastern Colombian cordillera. Our work constitutes the first example in which the Andean uplift coupled with gene flow influenced the evolutionary history of an arachnid lineage.

Phylogenomic insights into the diversification of salamanders in the Isthmura bellii group across the Mexican highlands

Mountain formation in Mexico has played an important role in the diversification of many Mexican taxa. The Trans-Mexican Volcanic Belt in particular has served as both a cradle of diversification and conduit for dispersal. We investigated the evolutionary history of the Isthmura bellii group of salamanders, a widespread amphibian across the Mexican highlands, using sequence capture of ultraconserved elements. Results suggest that the I. bellii group probably originated in southeastern Mexico in the late Miocene and later dispersed across the Trans-Mexican Volcanic Belt and into the Sierra Madre Occidental. Pre-Pleistocene uplift of the Trans-Volcanic Belt likely promoted early diversification by serving as a mesic land-bridge across central Mexico. These findings highlight the importance of the Trans-Volcanic Belt in generating Mexico's rich biodiversity.

Climate-induced glacier and snow loss imperils alpine stream insects

Climate warming is causing rapid loss of glaciers and snowpack in mountainous regions worldwide. These changes are predicted to negatively impact the habitats of many range-restricted species, particularly endemic, mountaintop species dependent on the unique thermal and hydrologic conditions found only in glacier-fed and snow melt-driven alpine streams. Although progress has been made, existing understanding of the status, distribution, and ecology of alpine aquatic species, particularly in North America, is lacking, thereby hindering conservation and management programs. Two aquatic insects - the meltwater stonefly (Lednia tumana) and the glacier stonefly (Zapada glacier) - were recently proposed for listing under the U.S. Endangered Species Act due to climate-change-induced habitat loss. Using a large dataset (272 streams, 482 total sites) with high-resolution climate and habitat information, we describe the distribution, status, and key environmental features that limit L. tumana and Z. glacier across the northern Rocky Mountains. Lednia tumana was detected in 113 streams (175 sites) within Glacier National Park (GNP) and surrounding areas. The probability of L. tumana occurrence increased with cold stream temperatures and close proximity to glaciers and permanent snowfields. Similarly, densities of L. tumana declined with increasing distance from stream source. Zapada glacier was only detected in 10 streams (24 sites), six in GNP and four in mountain ranges up to ~600 km southwest. Our results show that both L. tumana and Z. glacier inhabit an extremely narrow distribution, restricted to short sections of cold, alpine streams often below glaciers predicted to disappear over the next two decades. Climate warming-induced glacier and snow loss clearly imperils the persistence of L. tumana and Z. glacier throughout their ranges, highlighting the role of mountaintop aquatic invertebrates as sentinels of climate change in mid-latitude regions.

"Fix Me Another Marguerite!": Species delimitation in a group of intensively hybridizing lineages of ox-eye daisies (Leucanthemum Mill., Compositae-Anthemideae)

Delineating species boundaries in the framework of the multi-species coalescent (MSC) proves to be a reliable, objective, and reproducible method in an increasing number of studies. However, the underlying model assumes the lack of gene flow after speciation; an assumption which may be frequently violated in plant evolution. This study evaluates the robustness of currently available species delimitation methods implemented in beast (BFD, BFD*, and dissect) in the closely-knit ox-eye daisy group around Leucanthemum ageratifolium Pau. Comprising five taxa being allopatrically distributed between northern Spain and southern Italy this study group shows signs of hybridization with the widespread and codistributed species Leucanthemum vulgare (Vaill.) Lam. to various extent. As expected, our empirical analyses based on both AFLP fingerprinting and sequence data demonstrate that the robustness of species delimitation results is considerably influenced by the intensity of hybridization among species and the number of hybrid individuals included. Therefore, we set up a methodological pipeline with a first step of identification and subsequent removal of individuals showing admixed genetic patterns caused by actual interbreeding using AFLP-fingerprint and morphometric data, followed by application of different Bayesian MSC species delimitation methods based on the remnant individuals using both AFLP-fingerprint and sequence data (four nuclear markers, five concatenated intergenic spacer regions of the plastid genome). The results argue for acknowledgement of Leucanthemum laciniatum, L. legraeanum, and L. ligusticum as independent species, show the close relationship of L. ageratifolium, L. monspeliense, and L. vulgare, and give rise to the description of three nothospecies new to science.

Climate change and alpine stream biology: progress, challenges, and opportunities for the future

In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism-focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward-looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.