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Amazonia continuously reveals outstanding biotic diversity and endemism, but our comprehension regarding their underlying processes has been impaired by knowledge gaps on cryptic taxonomic diversity. Here, we clarified the diversity and historical biogeography of nurse‐frogs typical from Brazilian Southwestern Amazonia, the Allobates tinae species complex, using fine‐scale population sampling and molecular‐based analyses. Fieldwork was conducted at 23 localities across three major interfluves encompassing two well‐recognized areas of endemism. Fragments of three mitochondrial DNA genes were sequenced and compared through phylogeographic and phylogenetic analyses. Based on these results, we estimated the species limits and inferred the historical biogeography. We found seven highly supported clades, which were considered as distinct species according to delimitation analyses. However, only two of these clades are taxonomically described, indicating a nearly threefold underestimation of the complex species richness. Major clades showed pronounced genetic distances, strong spatial structuring, and restricted or absent haplotype sharing. However, genetic structure was not predicted by geographic distance, and strong genetic structure among major clades was evident even at smaller geographical scales lacking evident physical barriers. Biogeographic analysis indicated diversification of the A. tinae complex most likely occurred through dispersals followed by speciations. These events started southward from the Guiana Shield during the Miocene, and were followed by sequential secondary northward dispersals along the Pliocene and Pleistocene. Our results indicate combined roles of historical (landscape dynamism) and ecological (environmental heterogeneity) factors driving biotic diversification in Brazilian Southwestern Amazonia. [ABSTRACT FROM AUTHOR]

ABSTRACT A recent sequencing study has shown that two common Caribbean corals, Montastraea cavernosa and Siderastrea siderea, each consist of four genetically distinct lineages in the Florida Keys. These lineages are specialised to a certain depth and, to a lesser extent, to nearshore or offshore habitats. We hypothesised that the lineages' environmental specialisation is at least in part due to regulatory evolution, which would manifest as the emergence of groups of coregulated genes (‘modules’) demonstrating lineage‐specific responses to different reef environments. Our hypothesis also predicted that genes belonging to such modules would show greater genetic divergence between lineages than other genes. Contrary to these expectations, responses of cryptic lineages to natural environmental variation were essentially the same at the genome‐wide gene coexpression network level, with much fewer differences in gene expression between lineages compared to between habitats. Moreover, none of the identified coregulated gene expression modules exhibit elevated genetic divergence between lineages. Possible explanations of these unexpected results range from the leading role of algal symbionts and/or microbiome in adaptation to strong action of spatially varying selection equalising gene expression patterns despite different genetic background. We discuss how future studies could assist in discriminating between these possibilities. [ABSTRACT FROM AUTHOR]

We investigated population genetics of the native tree species Acer velutinum Boiss., Fagus orientalis Lipsky, and Quercus castaneifolia C.A. Mey. in the Hyrcanian forests of northern Iran and also F. orientalis populations in the Euro-Siberian and Colchic subregions of northern Türkiye. We used the double-digest RADseq method and genotyped 90 populations and 1,589 individuals across the distribution range of the species. Genome-wide SNPs from 28 populations of A. velutinum, 32 populations of F. orientalis, and 30 Q. castaneifolia revealed higher genetic differentiation among A. velutinum populations than among F. orientalis and Q. castaneifolia. The global FST value was lowest for F. orientalis populations and highest for A. velutinum populations, while the global FIS value was negative for A. velutinum. Demographic history analysis revealed a bottleneck during the last glacial period (11,500—115,000 Kya) for the A. velutinum populations with reduced effective population size (Ne). All three species show multiple bottlenecks and reduced Ne during the Quaternary. Pronounced genetic divergence among A. velutinum populations in the Hyrcanian forests compared to the other two species suggests cryptic speciation. Conversely, F. orientalis and Q. castaneifolia populations showed low levels of genetic structure, suggesting that species-specific factors, such as pollen production and pollination efficiency, may have influenced the genetic patterns within these species in similar environments. The nucleotide diversity of F. orientalis populations in Iran is negatively correlated with altitude (p = 0.046). In contrast, A. velutinum populations show a significant correlation between nucleotide diversity and longitude (p = 0.008). Furthermore, the F. orientalis populations from Türkiye showed a distinct west–east genetic structure and were highly diverged from the Iranian F. orientalis populations. [ABSTRACT FROM AUTHOR]

The Atlantic blue crab, Callinectes sapidus, is acknowledged as one of the worst invasive alien species in the Mediterranean, impacting biodiversity and human activities. Native to the western Atlantic, it has expanded to European coastal waters since the early 1900s. Despite its ecological and commercial importance, genetic research on this species is limited. Here we show a comprehensive investigation of the genetic variation and evolutionary history in Callinectes sapidus using 667 mitochondrial COI gene sequences. Our dataset encompasses 36 newly generated sequences from previously understudied Mediterranean sites and 631 from worldwide locations obtained from the GenBank public database. Our findings reveal two distinct, but closely related, genetic groups within the species' distribution range, suggesting the occurrence of a potential species complex. Furthermore, in the Mediterranean, low levels of genetic variability were observed except for substantial haplotypic differentiation in Turkish samples. This study depicts the global genetic diversity and evolutionary patterns of Callinectes sapidus, offering new insights into the taxonomic status of the species. [ABSTRACT FROM AUTHOR]

Cuscuta section Indecorae is an infrageneric clade of Cuscuta subgenus Grammica that originated in North America which includes three species: C. indecora, C. coryli, and C. warneri. Some forms of C. indecora are agricultural weeds, while C. warneri and C. coryli face conservation problems regionally or globally. Cuscuta indecora is a morphologically diverse species with three recognized varieties: C. indecora var. indecora, C. indecora var. longisepala, and C. indecora var. attenuata. Two recent broad-scale molecular phylogenetic studies raised questions about the circumscription of C. indecora and the validity of its infraspecific taxa. Therefore, we conducted an extensive morphometric study, and used DNA sequences from plastid and nuclear ribosomal non-coding regions to reconstruct evolutionary relationships among taxa. In addition, we studied the host range of all taxa using herbarium specimens, bipartite networks, and Venn diagrams. Results from all types of evidence confirmed the circumscription of the three species, but differed on the infraspecific structure of C. indecora. The molecular phylogeny inferred C. indecora as paraphyletic, consisting of two distinct clades, with C. coryli nested within one of them. The morphometric and host range studies uncovered extensive overlaps both among the traditional varieties of C. indecora as well as between the two molecular lineages of C. indecora. Previously, Iva annua had been considered the sole host of C. indecora var. attenuata (C. attenuata) and this presumed host specificity was the main criterion for accepting this taxon. We found that the type of C. indecora var. longisepala was also growing on Iva annua, which together with the morphological and genetical similarity, indicates that C. indecora var. attenuata is identical to C. indecora var. longisepala. Overall, considering the lack of morphological, host range, and geographical patterns distinguishing either the current three varieties of C. indecora or the two cryptic lineages, the most appropriate solution is to tentatively recognize C. indecora as variable species without recognizing any infraspecific taxa. [ABSTRACT FROM AUTHOR]

Ecological and geographical factors shape the current distribution of species. Analysing their interplay in a phylogenetic framework is key to understand the historical processes that have shaped the evolution of a group. Here, we modelled the ecological niches and geographic distributions of the five species of doraditos (Pseudocolopteryx spp.) to study their biogeographic histories, niche evolution and speciation process in a phylogenetic framework. Our potential distribution models uncovered novel range‐wide distributional patterns and seasonal movements in the doraditos, where four species are migratory with distinct breeding and non‐breeding distributions, and one (P. sclateri) exhibits a complex spatiotemporal distribution indicating nomadism. Ecological niche pairwise comparisons showed that none of the doraditos have equivalent niches and that niche differences are due to species‐specific habitat preferences. Phylogenetically weighted geographical and ecological analyses showed patterns of allopatric speciation and niche lability in the evolution of doraditos. The divergence of P. sclateri seems tied to its tropical‐to‐temperate wetland specialization. The montane P. acutipennis expanded to human‐modified lowlands following speciation, highlighting the need to control for post‐speciational changes in ecological niche comparisons as done here. In turn, P. dinelliana, P. citreola and P. flaviventris showed essentially allopatric breeding distributions, as a product of environmentally mediated divergence during their speciation processes. The distribution and migration data of the recently diverged cryptic sister species P. citreola and P. flaviventris are consistent with two possible speciation scenarios: peripatric speciation and migration dosing speciation. [ABSTRACT FROM AUTHOR]

Gymnurid rays are found in tropical, subtropical, and temperate regions around the world, where they are associated with sandy or muddy bottoms in coastal areas, being easily distinguished from other rays by the width of the disc. In recent years, the systematics of this family have been revised extensively. However, there has been no comprehensive molecular review of the family based on an adequate sample of species and localities, which may have obscured the presence of distinct evolutionary lineages. The present study was based on samples of 12 of the 13 valid species of the genus Gymnura, which were used for a multilocus reconstruction of the evolutionary history of the family Gymnuridae. Our results indicate the existence of several cryptic gymnurid lineages, within the species Gymnura micrura, Gymnura lessae, Gymnura altavela, and Gymnura poecilura. Also, we indicate that only half of the species that compose the genus are known, as well their conservation status. The analyses also indicate that the gymnurids originated during the Paleocene, with events of dispersal and vicariance occurring through the formation of oceanographic barriers, and species diversification peaking during the Oligocene and Miocene. The results of the present study reinforce the need for a comprehensive revision of the systematics of the family, in particular, the widely distributed species that are considered valid taxa, but may, in fact, represent different cryptic species. The inadequate classification of this cryptic diversity may have negative implications for the development of effective conservation measures. [ABSTRACT FROM AUTHOR]

The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change. The high species diversity in this mountain system has long been attributed to a complex set of factors, and recent large‐scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago (Mya) to the present. Despite our increasing understanding of the temporal mode of speciation, finer‐scale population‐level investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation. This is largely due to the dearth of organismal sampling among closely related species and populations, spanning the incredible size and topological heterogeneity of this region. Our study dives into these evolutionary dynamics of speciation using genomic and eco‐morphological data of Stellera chamaejasme L. We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages, suggesting a more recent diversification (~2.67–0.90 Mya), largely influenced by Pleistocene glaciation and biotic factors. These factors likely influenced allopatric speciation and advocated cyclical warming–cooling episodes along elevational gradients during the Pleistocene. The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity, necessitating increased conservation efforts. [ABSTRACT FROM AUTHOR]

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed. [ABSTRACT FROM AUTHOR]

The recent development of genetic methods has facilitated the identification of cryptic species across different groups of organisms, including plants. However, next‐generation sequencing has rarely been used to study cryptic speciation in plants, especially in bryophytes, organisms with a dominant haploid life phase. The ability to capture variation across the whole genome makes this method an effective tool for distinguishing cryptic lineages. We have focused on the genetic structure of the moss Meesia triquetra along the Alps‐to‐Scandinavia transect. We detected the presence of the two genetically critically different lineages of M. triquetra in Europe. These lineages overlap in both morphological characters of the gametophyte and distribution ranges. However, they considerably differ in ecological preferences to groundwater pH. While lineage 1 occupied alkaline to subneutral fens, lineage 2 occurred in fens saturated with neutral to acidic water. We consider the entities cryptic species with respect to genetic and ecological differences but the absence of morphological features necessary for determining the entities. We hypothesize that fragmentation of the ancestral population of the moss in geographically isolated refugia differing in the commonness of acidic and alkaline substrates led to consequent long‐term adaptation to different environmental conditions, then drove diversification in M. triquetra. [ABSTRACT FROM AUTHOR]

Speciation processes in the marine environment are often directly associated with vicariant events. In the case of loliginid squids (Cephalopoda: Loliginidae), these processes have been increasingly elucidated in recent years with the development of molecular technologies and increased sampling in poorly studied geographical regions, revealing a high incidence of cryptic speciation. Doryteuthis pealeii is a commercially important squid species for North Atlantic fisheries and has the second broadest geographic distribution in this genus. This study aimed to investigate the evolutionary history of this species and which biogeographic events may have influenced its diversification by assessing mitochondrial and nuclear markers. Our findings indicate that two previously detected lineages diverged from one another ~ 8 million years, compatible with the formation of the Caribbean and the establishment of the Amazon plume. Furthermore, separation between a North Atlantic and a Gulf of Mexico lineage during the Pleistocene period was noted. The inadequate classification of this cryptic diversity may have negative implications for the development of effective conservation and fisheries measures. [ABSTRACT FROM AUTHOR]

Uncertainties on species taxonomy and distribution are major factors hampering efficient conservation planning in the current context of biodiversity erosion, even concerning widespread and abundant species in relatively well‐studied regions. Species delimitation have long been based on phylogenetic analyses of a small number of standard markers, but accurate lineage identification through this approach can be hampered by incomplete lineage sorting, introgression or isolation by distance. In that context, analyses of introgression patterns at secondary contact zones offer an interesting alternative by allowing a direct estimation of reproductive isolation, especially when using genome‐wide markers. Here, we investigated a contact zone between two genetic groups of the Spiny‐footed Lizard Acanthodactylus erythrurus (Schinz, 1833) in Morocco, whose status as separate lineages remained disputed in previous multilocus studies. Based on thousands of genome‐wide markers obtained through a RADseq approach, we confirmed that they represent distinct evolutionary lineages. Furthermore, the transition at their contact zone was very steep, with spatially restricted gene flow, highlighting levels of reproductive isolation consistent with species‐level lineages. Our study further illustrates the power of RADseq‐based studies of contact zones to understand cryptic diversity in non‐model organisms. [ABSTRACT FROM AUTHOR]

The Atlantic blue crab, Callinectes sapidus, is acknowledged as one of the worst invasive alien species in the Mediterranean, impacting biodiversity and human activities. Native to the western Atlantic, it has expanded to European coastal waters since the early 1900s. Despite its ecological and commercial importance, genetic research on this species is limited. Here we show a comprehensive investigation of the genetic variation and evolutionary history in Callinectes sapidus using 667 mitochondrial COI gene sequences. Our dataset encompasses 36 newly generated sequences from previously understudied Mediterranean sites and 631 from worldwide locations obtained from the GenBank public database. Our findings reveal two distinct, but closely related, genetic groups within the species’ distribution range, suggesting the occurrence of a potential species complex. Furthermore, in the Mediterranean, low levels of genetic variability were observed except for substantial haplotypic differentiation in Turkish samples. This study depicts the global genetic diversity and evolutionary patterns of Callinectes sapidus, offering new insights into the taxonomic status of the species.

Species boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb‐I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY) and cytb genetic distance values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex. [ABSTRACT FROM AUTHOR]

Spondylidinae is a minor subfamily of Cerambycidae with around 100 species in 20 genera. The tribes Asemini and Spondylidini, both salient owing to vectors and invaders into the limelight of phytosanitary authorities, constitute the "spondylidine branch". Although a few species of the branch were being included in some higher taxonomic level studies, the phylogenetic relationships within the taxa have never been evaluated from a molecular viewpoint. The present study identifies the phylogenetic relationships within the branch inferring from a single locus (COI) global dataset and two multi-locus local datasets, binary combinations of mitochondrial COI, 16S rRNA and nuclear 28S rRNA D1-D2 , that sequences were obtained from the samples of the East of Marmara Region, Turkey. [(Spondylis+Neospondylis) + Megasemum ] and [ Tetropium+Asemum ] groups were separated from the same node in the phylogenetic trees. The genus Cephalallus was stated on the basalmost of these two groups. Arhopalus split from all other genera and divided into two subgroups. There were discrepancies between morphology and COI barcode sequences, which might be a sign of hybridisation between A. rusticus and A. syriacus. Intraspecific distances of COI gene regions of S. buprestoides, As. striatum and T. cinnamopterum were up to 4.26%, 8.51%, and 6%, respectively, which might point out to cryptic speciation. [ABSTRACT FROM AUTHOR]

DNA sequences for adult and larval Allocreadium spp. from their natural fish and molluscan hosts were generated. Phylogenetic analyses based on two molecular markers (ITS2 and 28S rDNA) yielded unexpected results regarding the diversity and life cycles of European species. It was found that specimens morphologically consistent with the concept of Allocreadium isoporum (Looss 1894) form two different species-level genetic lineages. For now, the morphological differences between the specimens belonging to different genetic lineages are not discernible; they can infect the same fish species at the same or different localities. However, the species differ in their life-cycle patterns, specifically in terms of larval stages and first intermediate host specificity. Based on molecular markers, the tailed ophthalmoxiphidiocercaria developing in Pisidium spp. was associated with a sexual adult A. isoporum from Alburnus alburnus, Barbatula barbatula and Rutilus rutilus. Representatives of another genetic lineage, recovered from R. rutilus and Scardinius erythrophthalmus, turned out to be conspecific with the enigmatic European larval trematode Cercariaeum crassum Wesenberg-Lund, 1934, from the sphaeriid bivalve Pisidium amnicum. This finding requires the recognition of the cryptic species Allocreadium crassum. [ABSTRACT FROM AUTHOR]

In Big Cypress National Preserve, the federally threatened Everglades bully (Sideroxylon reclinatum subsp. austrofloridense) is sympatric with its conspecific, more widespread relative, the Florida bully (Sideroxylon reclinatum subsp. reclinatum). In this area of overlap, the only reliable characters to distinguish the two are cryptic, micromorphological traits of the abaxial laminar surface. In order to better understand the distribution of the federally threatened taxon, we used a combination of habitat suitability modeling (HSM), field surveys, and microscopy. Using models to inform initial surveys, we collected leaf material of 96 individuals in the field, 86 of which we were able to identify to subspecies. Of these, 73 (85%) were identified as the threatened taxon, expanding both the known range and population size within Big Cypress. We used these 73 new occurrences to rerun HSMs to create a more accurate picture of where the taxon is likely to occur. A total of 15,015 hectares were predicted to be suitable habitat within Big Cypress, with 34,069 hectares across the entire study area. These model results could be used to inform the critical habitat designation for this taxon. For at-risk, cryptic taxa, such as the Everglades bully, multiple approaches are needed to inform management and conservation priorities, including the consideration of a hybridization zone. [ABSTRACT FROM AUTHOR]

Abstract Species boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb‐I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY) and cytb genetic distance values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex.

Until a few years ago, Sphagnum magellanicum was understood to be a single widespread species with an intercontinental range. Recent work by Norwegian sphagnologists showed that S. magellanicum s.str. is restricted to southern South America and plants known as S. magellanicum in Europe should be referred to S. divinum and S. medium. In a separate publication, we showed that there are two additional major clades in eastern North America, and we describe them herein as S. diabolicum and S. magniae. These species are very hard to distinguish morphologically (and also from S. divinum and S. medium) but are distinct phylogenetically, ecologically and geographically, and are important units of biodiversity. Morphological variation within and between species is photographically documented. [ABSTRACT FROM AUTHOR]

The European Robin Erithacus rubecula is currently treated as a single species with eight subspecies. A previous molecular study and new molecular, morphometric and bioacoustic data reported here strongly support the recognition of three species in this complex: E. rubecula (Europe, North Africa and Macaronesia except the central Canary Islands), E. superbus (Tenerife) and a recently described subspecies on Gran Canaria which we raise to species rank as E. marionae. The taxa on Tenerife and Gran Canaria have previously been lumped as a single taxon but differ from each other and from E. rubecula in territorial songs, tic calls, seep calls and wing length. All three species are characterised by moderate to high levels of interspecific mitochondrial DNA sequence divergence (mean 4.2–4.8%). Phylogenetic analysis indicates that E. marionae is sister to E. superbus + E. rubecula. Recognition of Gran Canaria and Tenerife Robins as separate species adds two single‐island endemics to the Canary Islands avifauna. [ABSTRACT FROM AUTHOR]

The bonnethead Sphyrna tiburo is a wide-spread, small species of coastal hammerhead shark with a long history of taxonomic uncertainty, including, according to some authors, disjoint subspecies in the western Atlantic and eastern Pacific oceans. The present study investigates the level of morphometric and genetic variation within the Sphyrna tiburo complex throughout most of its distributional range including the western Atlantic, the Gulf of Mexico, the Caribbean, and the eastern Pacific. A morphometric study, including a comparison of ampullary densities, and a molecular analysis of two mitochondrial genes, was performed. We analyzed variation in cephalofoil shape between and within lineages, based on landmarks and Fourier analysis of the silhouettes. All tests delineated discrete morphological groups, including differences of ampullae density for those lineages in which this information could be unambiguously assessed. Both morphometric and molecular analysis support the existence of three different evolutionarily significant units (two in the Atlantic: one northern and one south-central, and a third in the eastern Pacific) that deserve specific taxonomic status. We urge a deep taxonomic review of this complex to gather biological data on each lineage and develop adequate independent conservation strategies and actions to protect the various evolutionary units. [ABSTRACT FROM AUTHOR]

The southern Appalachian Mountains are a biodiverse region with high levels of endemism. Shared biogeographic patterns among co-distributed, but independent taxa might illuminate common drivers of Appalachian endemism. Lathrobium is a Holarctic genus with 38 species described form North America, six of which are flightless and endemic to the high Appalachians. We use an integrative morphological and multi-locus molecular dataset to study phylogenetic and biogeographical relationships of Appalachian Lathrobium and test subgeneric hypotheses. A phylogeny based on 176 samples from 67 taxa supported three independent arrivals in the Appalachian Mountains. Divergence times estimated in BEAST2 were concurrent for all three lineages and fell between the Miocene or early Pliocene (16.4 - 4.6 Ma). Speciation within Appalachians occurred during the Pleistocene (2.3 - 0.1 Ma). Monophyly of existing subgenera was supported except for Abletobium Casey. Abletobium is placed in synonymy with Glyptomerus Müller. Our results reveal the importance of cold-climate refugia within the Appalachian Mountains for the persistence and in-situ diversification of endemic endogean taxa. We hypothesize that the xeric climate of the Miocene drove Lathrobium lineages into the mountains and subsequent isolation in mountaintop refugia during warm Pleistocene interglacials led to speciation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The barnacle Lepas anatifera Linnaeus, 1758 (Scalpellomorpha, Lepadidae) is a worldwide distributed species. For investigating its genetic diversity in the northwest Pacific, two complete mitochondrial genomes were determined and analyzed. The lengths of the two complete mitogenomes were 15,708 bp and 15,703 bp, respectively. Both of them contained typical 37 genes with an identical order to L. anserifera Linnaeus, 1767 and L. australis Darwin, 1851 mitogenome. Except for ND1 and ND2, 11 protein-coding genes (PCGs) started with an ATN initiation codon (ATA, ATG, ATC, and ATT). Twelve PCGs were terminated with TAA or TAG stop codon, whereas ND1 possessed an incomplete termination codon (T–). Phylogenetic analysis revealed that L. australis and L. anserifera clustered together, and then with L. anatifera. The distinct genetic distances (0.17) based on concatenated sequence of 13 PCGs between the two mitogenomes of L. anatifera suggest the existence of cryptic speciation. Additional samples from multiple localities should be collected and analyzed to deepen the understanding of cryptic diversity within the northwest Pacific.

Connectivity among populations of widespread marine species is expected to be correlated with their dispersal potential but the evolution of reproductive barriers may account for variations in spatial genetic patterns. Marine benthic hydroid species are traditionally considered widespread, with long-distance rafting presumably increasing their dispersal potential. In this study, we investigated the relationship between genetic, morphological and environmental variability within three benthic marine hydroid species to evaluate current patterns of genetic variation and assess the existence of cryptic speciation. Although a long-lived planktonic stage is absent in all the lineages sampled and they have an overlapping geographical ranges, we observed contrasting patterns of genetic and phenotypic divergence: Orthopyxis sargassicola showed little genetic variation, while O. caliculata and O. crenata each contained high genetic differentiation, primarily suggesting limited dispersal potential. Significant covariation was observed between phenotypic and environmental data in all lineages, but different environmental variables were responsible for explaining morphological variation in each case. Genetic and morphological patterns within O. caliculata and O. crenata are suggestive of cryptic speciation, while phenotypic variation in O. sargassicola may be plastic. Thus, morphological and genetic patterns may potentially vary among related marine lineages with shared life history traits and habitat. [ABSTRACT FROM AUTHOR]

Aim: Specialisation to the soil environment is expected to constrain the spatial scale of diversification within animal lineages. In this context, flightless arthropod lineages, adapted to soil environments, but with broad geographical ranges, represent something of an anomaly. Here we investigate the diversification process within one such 'anomalous' soil specialist, an eyeless and flightless beetle species strongly adapted to the endogean environment but distributed across several oceanic islands. Location: Canary Islands. Taxon: Geomitopsis franzi Coiffait, 1978 (Coleoptera, Staphylinidae). Methods: We performed an integrative study, including molecular phylogenetics, population genomics and morphometry. Four DNA regions (two mitochondrial and two nuclear) were amplified and sequenced for 159 specimens from 58 localities sampled across five islands for phylogenetic analyses, and a dated phylogenetic tree was obtained using a mitogenome dataset. ddRAD‐seq data were generated to evaluate mtDNA lineages in sympatry against the biological species concept. Results: We found high levels of genetic differentiation (>8% COI gene divergence) among populations from different islands and among geographically coherent lineages within single islands. Lineages within Tenerife presented significant patterns of isolation by distance, with ddRAD‐seq providing evidence that lineages represent biological species. Morphometric analyses revealed limited variation. Main conclusions: Geomitopsis franzi is comprised of at least seven lineages that merit consideration as biological species, and is best considered as a complex of cryptic species. The limited morphological variation across these lineages is consistent with adaptation to the endogean environment placing strong constraints on morphological change. The evolution of cryptic species should be favoured when such constraints are coupled with limited dispersal ability, a trait that broadly characterises the soil mesofauna. [ABSTRACT FROM AUTHOR]

Distinguishing between populations with strong genetic structure and unique species is a common challenge in systematics, especially for taxa occurring in fragmented habitats where allopatric speciation may be widespread and distinct groups may be morphologically similar. Such is often the case with species complexes across sky island environments. In these scenarios, biogeography may help to explain the taxonomic relations between species complex members, and restriction site-associated DNA (RAD) sequencing methods are commonly used to compare closely related taxa across thousands of loci. Here we use RADseq to clarify the boundaries separating the geographically distinct but morphologically similar varieties of the Primula cusickiana species complex, and to contextualize past findings of strong genetic structure among populations within varieties. Our genetic analyses demonstrate pronounced separation between isolated populations of this Great Basin endemic, indicating that the current varietal classification of complex members is inaccurate, and emphasizing their conservation importance. We discuss how these results correspond to recent biogeographical models used to describe the distribution of other sky island taxa in western North America. Our findings also fit into a wider trend observed for alpine Primula species complexes, and we consider how edaphic specialization and heterostylous breeding systems may be contributing to frequent diversification via allopatric speciation in this genus. [ABSTRACT FROM AUTHOR]

Abstract Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow‐up study required to verify their geographic or evolutionary limits. Here, we follow‐up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species’ range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome‐wide divergence (FST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species’ range. Within lineages, gene flow was high, with low differentiation (mean FST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non‐contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.

DNA sequences for adult and larval Allocreadium spp. from their natural fish and molluscan hosts were generated. Phylogenetic analyses based on two molecular markers (ITS2 and 28S rDNA) yielded unexpected results regarding the diversity and life cycles of European species. It was found that specimens morphologically consistent with the concept of Allocreadium isoporum (Looss 1894) form two different species-level genetic lineages. For now, the morphological differences between the specimens belonging to different genetic lineages are not discernible; they can infect the same fish species at the same or different localities. However, the species differ in their life-cycle patterns, specifically in terms of larval stages and first intermediate host specificity. Based on molecular markers, the tailed ophthalmoxiphidiocercaria developing in Pisidium spp. was associated with a sexual adult A. isoporum from Alburnus alburnus, Barbatula barbatula and Rutilus rutilus. Representatives of another genetic lineage, recovered from R. rutilus and Scardinius erythrophthalmus, turned out to be conspecific with the enigmatic European larval trematode Cercariaeum crassum Wesenberg-Lund, 1934, from the sphaeriid bivalve Pisidium amnicum. This finding requires the recognition of the cryptic species Allocreadium crassum.

Background and aimsThe broomrapes, Orobanche sensu lato (Orobanchaceae), are common root parasites found across Eurasia, Africa and the Americas. All species native to the western hemisphere, recognized as Orobanche sections Gymnocaulis and Nothaphyllon, form a clade that has a centre of diversity in western North America, but also includes four disjunct species in central and southern South America. The wide ecological distribution coupled with moderate taxonomic diversity make this clade a valuable model system for studying the role, if any, of host-switching in driving the diversification of plant parasites.MethodsTwo spacer regions of ribosomal nuclear DNA (ITS + ETS), three plastid regions and one low-copy nuclear gene were sampled from 163 exemplars of Orobanche from across the native geographic range in order to infer a detailed phylogeny. Together with comprehensive data on the parasites' native host ranges, associations between phylogenetic lineages and host specificity are tested.Key resultsWithin the two currently recognized species of O. sect. Gymnocaulis, seven strongly supported clades were found. While commonly sympatric, members of these clades each had unique host associations. Strong support for cryptic host-specific diversity was also found in sect. Nothaphyllon, while other taxonomic species were well supported. We also find strong evidence for multiple amphitropical dispersals from central North America into South America.ConclusionsHost-switching is an important driver of diversification in western hemisphere broomrapes, where host specificity has been grossly underestimated. More broadly, host specificity and host-switching probably play fundamental roles in the speciation of parasitic plants.

Integrative taxonomic studies continue to reveal that many current polytypic species of birds are in fact constituted by two or more species and therefore have been central in uncovering 'hidden' or 'cryptic' biodiversity. The Olivaceous Flatbill (Aves: Tyrannidae: Rhynchocyclus olivaceus) currently has nine recognized subspecies distributed throughout the Neotropics, but so far, no complete phylogenetic hypothesis exists to test the validity and evolutionary relationships among them. To remedy this, we conducted a multi‐character integrative taxonomic revision of the genus Rhynchocyclus, focusing on the polytypic R. olivaceus. The combination of a taxonomically dense sampled multilocus phylogeny (including three mitochondrial and two nuclear genes) with phenotypic analyses including morphological and vocal characters pointed to several taxonomic inconsistencies within R. olivaceus. The analyses strongly support that R. olivaceus is paraphyletic, with an exclusively cis‐Andean clade (where the topotypic R. olivaceus is found) clustering as sister to Rhynchocyclus fulvipectus, to the exclusion of a clade grouping trans‐Andean and western Amazonian populations currently placed in R. olivaceus—one of which is unnamed and fully diagnosable based on vocal and genetic characters. Consistent with the phylogenetic results, our vocal analyses identified at least four morphologically cryptic lineages within R. olivaceus that can be mutually diagnosed from each other by different loudsongs and call parameters. Therefore, we provide evidence for splitting these four groups into separate species, two of which are sympatric but not syntopic in western Amazonia, including an unnamed species described herein—Rhynchocyclus cryptus, sp. nov. urn:lsid:zoobank.org:act:2DC17190‐2BDD‐49EC‐88E6‐4CF2FC2562A3. [ABSTRACT FROM AUTHOR]

Phylogenetic hypotheses for the peracarid order Cumacea are scarce and have not provided a solution to the full extent. In the present study, a fragment of the mitochondrial 16S rDNA was used to erect a phylogenetic hypothesis for three cumacean families, Diastylidae, Bodotriidae and Leuconidae, along with intra-family relationships of the latter. The Cumacea resolved monophyletic with tanaids and isopods as outgroup taxa. The Diastylidae were the only family with good support for monophyly. The genus Leucon resolved paraphyletic, whereas the subgenus Crymoleucon was monophyletic. Furthermore, the genetic structure was analysed for two leuconid species, Leucon antarcticus Zimmer, 1907 and L. intermedius Mühlenhardt-Siegel, 1996, from the Weddell Sea and the Ross Sea. The two species showed different patterns of intraspecific genetic variability. In contrast to L. intermedius, a bimodal distribution of pairwise genetic distances was observed for L. antarcticus, which is correlated with geographical and depth distributions between the Ross Sea and the Weddell Sea. Although a clear evaluation of cryptic speciation in these species requires additional work on more specimens from more geographic regions and broader depth ranges, differences shown in the sequences of 16S rDNA can only be explained by genetic separation of populations between the Weddell Sea and the Ross Sea for an extended period of time.

Abstract The trahira or wolf fish - Hoplias malabaricus- is a valid species, although recent cytogenetic and molecular studies have indicated the existence of a species complex. In this context, the present study analyzed the mitochondrial COI marker to determine the levels of genetic diversity of specimens from the Brazilian state of Maranhão, and verify the occurrence of distinct lineages within the study area. Samples were collected from the basins of the Turiaçu, Pindaré, Mearim, Itapecuru, and Parnaíba rivers. A 630-bp fragment was obtained from 211 specimens, with 484 conserved and 108 variable sites, and 60 haplotypes (Hd = 0,947; π = 0,033). The phylogenetic analyses indicated the existence of three distinct lineages of H. malabaricus from Maranhão. Genetic distances of 1.5-8.2% were found between all the populations analyzed, while the variation between haplogroups ranged from 2.1% to 7.7%. The AMOVA indicated that most of the molecular variation was found among groups, with high FST values. The high levels of genetic variability found in the present study are supported by the available cytogenetic data. These findings reinforce the need for the development of effective programs of conservation and management independently for each river basin, in order to preserve the genetic variability found in this taxon.

Abstract Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo‐West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological‐scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation.

In Big Cypress National Preserve, the federally threatened Everglades bully (Sideroxylon reclinatum subsp. austrofloridense) is sympatric with its conspecific, more widespread relative, the Florida bully (Sideroxylon reclinatum subsp. reclinatum). In this area of overlap, the only reliable characters to distinguish the two are cryptic, micromorphological traits of the abaxial laminar surface. In order to better understand the distribution of the federally threatened taxon, we used a combination of habitat suitability modeling (HSM), field surveys, and microscopy. Using models to inform initial surveys, we collected leaf material of 96 individuals in the field, 86 of which we were able to identify to subspecies. Of these, 73 (85%) were identified as the threatened taxon, expanding both the known range and population size within Big Cypress. We used these 73 new occurrences to rerun HSMs to create a more accurate picture of where the taxon is likely to occur. A total of 15,015 hectares were predicted to be suitable habitat within Big Cypress, with 34,069 hectares across the entire study area. These model results could be used to inform the critical habitat designation for this taxon. For at-risk, cryptic taxa, such as the Everglades bully, multiple approaches are needed to inform management and conservation priorities, including the consideration of a hybridization zone.

Recent studies in eastern Amazon coastal drainages and their surroundings have revealed new fish species that sometimes exhibit little morphological differentiation (cryptic species). Thus, we used a DNA-based species delimitation approach to test if populations showing the morphotype and typical character states of the Aphyocharax avary holotype correspond either to A. avary or A. brevicaudatus, two known species from the region, or if they form independent lineages, indicating cryptic speciation. WP and GMYC analyses recovered five lineages (species) in the ingroup, while a bPTP analysis delimited three lineages. ABGD analyses produced two possible results: one corroborating the WP and GMYC methods and another corroborating the bPTP method. All methods indicate undescribed cryptic species in the region and show variation from at least 1 to 4 species in the ingroup, depending on the approach, corroborating previous studies, and revealing this region as a possible hotspot for discovering undescribed fish species. [ABSTRACT FROM AUTHOR]

The heteronemertean Cerebratulus marginatus Renier, 1804 is a well-known representative of the family Lineidae (Nemertea) inhabiting sandy or muddy sediments throughout the world. Due to its wide geographic distribution and the lack of distinctive external morphological features among different populations, the species has been considered cosmopolitan. Increasing evidence indicates that nemertean species, including Cerebratulus marginatus, described based on morphology are often not supported by genetic data and represent complexes of cryptic species, rather than cosmopolitan species. Here, we use species delimitation and phylogenetic analyses to evaluate the speciation patterns within the putative C. marginatus species complex. We examined 25 specimens morphologically ascribed to C. marginatus and closely related species using a multilocus dataset including two mitochondrial markers (16S rRNA, COI) and three nuclear markers (18S rRNA, 28S rRNA, H3). Our analyses identified at least four supported independent lineages among the populations analysed, indicating that samples identified as C. marginatus might represent indeed a complex of cryptic species. Therefore, our results do not support the cosmopolitanism of C. marginatus and provide additional evidence suggesting that species identifications in nemerteans should not be based exclusively on morphological or anatomical features which do not accurately reflect evolutionary patterns. Our study highlights the importance of including molecular data in addition to morphological information to accurately delimit species boundaries, thereby improving nemertean taxonomy by providing a more accurate picture of the true species diversity and geographic distribution of this typically neglected phylum. [ABSTRACT FROM AUTHOR]

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Abstract Recent studies in eastern Amazon coastal drainages and their surroundings have revealed new fish species that sometimes exhibit little morphological differentiation (cryptic species). Thus, we used a DNA-based species delimitation approach to test if populations showing the morphotype and typical character states of the Aphyocharax avary holotype correspond either to A. avary or A. brevicaudatus, two known species from the region, or if they form independent lineages, indicating cryptic speciation. WP and GMYC analyses recovered five lineages (species) in the ingroup, while a bPTP analysis delimited three lineages. ABGD analyses produced two possible results: one corroborating the WP and GMYC methods and another corroborating the bPTP method. All methods indicate undescribed cryptic species in the region and show variation from at least 1 to 4 species in the ingroup, depending on the approach, corroborating previous studies, and revealing this region as a possible hotspot for discovering undescribed fish species.

Molecular studies have shown that many polytypic species of birds are paraphyletic and may actually consist of multiple independent species, some of them phenotypically cryptic. One of such cases is Dendrocolaptes picumnus, which was found to be a paraphyletic species, with Dendrocolaptes hoffmannsi nested in it. Recent evidence also showed that multiple independent evolutionary lineages exist in the polytypic D. picumnus that may be characterized as distinct species, however, conclusions were weakened due to small sample sizes. To further evaluate phylogenetic relationships, species limits, and the diversification history of the D. picumnus species complex, herein we performed the densest sampling ever registered for the complex, and analyzed sequences of mitochondrial and nuclear genes from 106 specimens, belonging to all but four taxa grouped in the complex. Our phylogenetic analyses confirmed the monophyly of D. hoffmannsi and D. platyrostris, as well as the paraphyly of the polytypic D. picumnus. A combination of coalescent and population genetic structure analyses further supported an evolutionary independent status for D. picumnus transfasciatus, but were ambiguous with respect to the statuses of nominate D. picumnus, D. picumnus pallescens, D. picumnus validus, and D. picumnus costaricensis. In contrast, D. picumnus olivaceus and D. platyrostris intermedius were polyphyletic and not genetically structured with respect to D. picumnus pallescens and D. platyrostris platyrostris, respectively. Our results did not support the monophyly of the previously defined 'Amazonian' and 'montane' subspecies groups of D. picumnus, further indicating that at least one 'montane' taxon may actually belong to the 'Chaco' group, a relationship that highlights a close historical connection between the Andean and Chacoan biotas. When interpreted together with previous morphological studies, our results support the split of the polytypic D. picumnus into at least two species, while keeping the status of D. hoffmannsi and D. platyrostris as distinct species. [ABSTRACT FROM AUTHOR]

Background: Seisonidea (also Seisonacea or Seisonidae) is a group of small animals living on marine crustaceans (Nebalia spec.) with only four species described so far. Its monophyletic origin with mostly free-living wheel animals (Monogononta, Bdelloidea) and endoparasitic thorny-headed worms (Acanthocephala) is widely accepted. However, the phylogenetic relationships inside the Rotifera-Acanthocephala clade (Rotifera sensulato or Syndermata) are subject to ongoing debate, with consequences for our understanding of how genomes and lifestyles might have evolved. To gain new insights, we analyzed first drafts of the genome and transcriptome of the key taxon Seisonidea. Results: Analyses of gDNA-Seq and mRNA-Seq data uncovered two genetically distinct lineages in Seison nebaliae Grube, 1861 off the French Channel coast. Their mitochondrial haplotypes shared only 82% sequence identity despite identical gene order. In the nuclear genome, distinct linages were reflected in different gene compactness, GC content and codon usage. The haploid nuclear genome spans ca. 46 Mb, of which 96% were reconstructed. According to ~ 23,000 SuperTranscripts, gene number in S. nebaliae should be within the range published for other members of Rotifera-Acanthocephala. Consistent with this, numbers of metazoan core orthologues and ANTP-type transcriptional regulatory genes in the S. nebaliae genome assembly were between the corresponding numbers in the other assemblies analyzed. We additionally provide evidence that a basal branching of Seisonidea within Rotifera-Acanthocephala could reflect attraction to the outgroup. Accordingly, rooting via a reconstructed ancestral sequence led to monophyletic Pararotatoria (Seisonidea+Acanthocephala) within Hemirotifera (Bdelloidea+Pararotatoria). Conclusion: Matching genome/transcriptome metrics with the above phylogenetic hypothesis suggests that a haploid nuclear genome of about 50 Mb represents the plesiomorphic state for Rotifera-Acanthocephala. Smaller genome size in S. nebaliae probably results from subsequent reduction. In contrast, genome size should have increased independently in monogononts as well as bdelloid and acanthocephalan stem lines. The present data additionally indicate a decrease in gene repertoire from free-living to epizoic and endoparasitic lifestyles. Potentially, this reflects corresponding steps from the root of Rotifera-Acanthocephala via the last common ancestors of Hemirotifera and Pararotatoria to the one of Acanthocephala. Lastly, rooting via a reconstructed ancestral sequence may prove useful in phylogenetic analyses of other deep splits. [ABSTRACT FROM AUTHOR]

Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed. [ABSTRACT FROM AUTHOR]

The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI : π = 0.18, hd = 0.99; ANT : π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities. [ABSTRACT FROM AUTHOR]

Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow‐up study required to verify their geographic or evolutionary limits. Here, we follow‐up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species' range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome‐wide divergence (FST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species' range. Within lineages, gene flow was high, with low differentiation (mean FST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non‐contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation. [ABSTRACT FROM AUTHOR]

The barnacle Lepas anatifera Linnaeus, 1758 (Scalpellomorpha, Lepadidae) is a worldwide distributed species. For investigating its genetic diversity in the northwest Pacific, two complete mitochondrial genomes were determined and analyzed. The lengths of the two complete mitogenomes were 15,708 bp and 15,703 bp, respectively. Both of them contained typical 37 genes with an identical order to L. anserifera Linnaeus, 1767 and L. australis Darwin, 1851 mitogenome. Except for ND1 and ND2, 11 protein-coding genes (PCGs) started with an ATN initiation codon (ATA, ATG, ATC, and ATT). Twelve PCGs were terminated with TAA or TAG stop codon, whereas ND1 possessed an incomplete termination codon (T–). Phylogenetic analysis revealed that L. australis and L. anserifera clustered together, and then with L. anatifera. The distinct genetic distances (0.17) based on concatenated sequence of 13 PCGs between the two mitogenomes of L. anatifera suggest the existence of cryptic speciation. Additional samples from multiple localities should be collected and analyzed to deepen the understanding of cryptic diversity within the northwest Pacific. [ABSTRACT FROM AUTHOR]

Understanding the mechanisms underlying species divergence remains a central goal in evolutionary biology. Landscape genetics can be a powerful tool for examining evolutionary processes. We used genome‐wide scans to genotype samples from populations of eight Angophora species. Angophora is a small genus within the eucalypts comprising common and rare species in a heterogeneous landscape, making it an appropriate group to study speciation. We found A. hispida was highly differentiated from the other species. Two subspecies of A. costata (subsp. costata and subsp. euryphylla) formed a group, while the third (subsp. leiocarpa, which is only distinguished by its smooth fruits and provenance) was supported as a distinct pseudocryptic species. Other species that are morphologically distinct could not be genetically differentiated (e.g., A. floribunda and A. subvelutina). Distribution and genetic differentiation within Angophora were strongly influenced by temperature and humidity, as well as biogeographic barriers, particularly rivers and higher elevation regions. While extensive introgression was found between many populations of some species (e.g., A. bakeri and A. floribunda), others only hybridized at certain locations. Overall, our findings suggest multiple mechanisms drove evolutionary diversification in Angophora and highlight how genome‐wide analyses of related species in a diverse landscape can provide insights into speciation. [ABSTRACT FROM AUTHOR]

The definition of species boundaries constitutes an important challenge in biodiversity studies. Cynopoecilus Regan, 1912 encompasses several endangered species of annual fish, occurring in temporary ponds in a restricted area of Southern Brazil and Uruguay. Divergences about the taxonomic status of Cynopoecilus species highlight the importance of species delimitation studies. Therefore, we address here the phylogenetic structure of Cynopoecilus, while assessing its taxonomic implications. For this, fragments of the mitochondrial COI and nuclear RAG1 genes were characterized and analyzed for a set of 275 and 280 specimens, respectively. DNA barcoding and phylogenetic analyses detected subdivision of these specimens in 8–10 clusters, which comprise the six previously described species, and suggest one invalid taxon and at least 3–5 putative new species. The phylogenetic structure also suggests that the Jacuí River and the Patos Lagoon historically acted as effective barriers to gene flow between populations, although some isolated dispersal events across these water bodies could be evidenced, especially for C. melanotaenia Regan, 1912. In general, the results highlight the need of independent conservation strategies within the distribution area of each of the endemic allopatric killifish clusters, while questioning several taxonomic boundaries and distribution data. [ABSTRACT FROM AUTHOR]

• High COI nucleotide diversity (10.70%) of Rhagium inquisitor was determined. • In the global assemblage the main lineages were Americans and Eurasians. • The shared haplotype of Europe was sampled at the east of the Marmara Basin. The increased volume of intercontinental-trade had facilitated the distribution of species, including invaders. Wooden packaging materials, goods and timber are being transported via international ports in East of the Marmara Basin, where has vast forests. That forests provide an appropriate-mediator for the introduction and invasion of wood-boring insects, which are the most common group being transported between continents. One of them is Rhagium inquisitor , which has a pivotal role in wood decay, nevertheless, it is detrimental for industrial wood. We analyzed the 654 bp length of cytochrome c oxidase I (COI) gene, to determine native and introduced haplotypes of the ribbed-pine-borer, to investigate their phylogenetic relationships and possibly cryptic speciation of the morphospecies. It was found out that sixteen haplotypes were divided into five haplogroups. The groups were assembled on two main lineages: Eurasian and American. The genetic distance between the American (Groups 1–3), Asian (Group-4) and European (Group-5) clusters ranged from 3 to 10%; between haplotypes ranged from 0.2 to 10.9%. The distances between the specimens of the Marmara Basin (H9-12, Group-4) were lower compared to H16, which nested in Group-5. That haplotype was sampled on imported timber and was found out that it is shared between France, Germany, Italy, and Austria. Maximum Likelihood, Neighbor-Joining and Bayesian Inference trees showed the same topologies, and Median-Joining network also supported them. Contrary to the usual, our findings point out that some species might have been introduced from Europe to Asia. Furthermore, the high genetic diversity of the bark-runner between continents could be a sign of cryptic-allopatric speciation. [ABSTRACT FROM AUTHOR]

Understanding the role of dispersal and adaptation in the evolutionary history of marine species is essential for predicting their response to changing conditions. We analyzed patterns of genetic differentiation in the key tropical calcifying species of large benthic foraminifera Amphistegina lobifera to reveal the evolutionary processes responsible for its biogeographic distribution. We collected specimens from 16 sites encompassing the entire range of the species and analyzed hypervariable fragments of the 18S SSU rDNA marker. We identified six hierarchically organized genotypes with mutually exclusive distribution organized along a longitudinal gradient. The distribution is consistent with diversification occurring in the Indo‐West Pacific (IWP) followed by dispersal toward the periphery. This pattern can be explained by: (a) high dispersal capacity of the species, (b) habitat heterogeneity driving more recent differentiation in the IWP, and (c) ecological‐scale processes such as niche incumbency reinforcing patterns of genotype mutual exclusion. The dispersal potential of this species drives the ongoing range expansion into the Mediterranean Sea, indicating that A. lobifera is able to expand its distribution by tracking increases in temperature. The genetic structure reveals recent diversification and high rate of extinction in the evolutionary history of the clade suggesting a high turnover rate of the diversity at the cryptic level. This diversification dynamic combined with high dispersal potential, allowed the species to maintain a widespread distribution over periods of geological and climatic upheaval. These characteristics are likely to allow the species to modify its geographic range in response to ongoing global warming without requiring genetic differentiation. [ABSTRACT FROM AUTHOR]

Study of the congruence of population genetic structure between hosts and pathogens gives important insights into their shared phylogeographical and coevolutionary histories. We studied the population genetic structure of castrating anther‐smut fungi (genus Microbotryum) and of their host plants, the Silene nutans species complex, and the morphologically and genetically closely related Silene italica, which can be found in sympatry. Phylogeographical population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant–pathogen pairs of anther‐smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic single nucleotide polymorphisms. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC‐RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with that previously inferred for the host plant and probably occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of individual host–pathogen pairs contribute to a better understanding of co‐evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies remain scarce. [ABSTRACT FROM AUTHOR]

Pteropyrum is a small genus of Polygonaceae with four species from the arid regions of Iran and adjacent countries. Pteropyrum spp. are not precisely delimitated and are difficult to identify because of their high plasticity in morphological characters. Pteropyrum (C3) has a close affinity to Calligonum (C4) and is therefore a suitable case for C4 evolutionary studies. We investigated the morphology and micromorphology (including pollen morphology) of Pteropyrum and elucidated the phylogenetic relationships with Atraphaxis and Calligonum using nuclear ITS sequences. Characteristics of the photosynthetic tissues such as volume and number of layers of primary carbon assimilation tissues (PCA) and photosynthetic carbon reduction tissue (PCR) were studied. In addition, the leaf and cotyledon anatomical characters of Pteropyrum (C3), Atraphaxis (C3) and Calligonum (C4), and their δ 13C values were compared to look for evolutionary changes in assimilating organs. The molecular phylogenetic tree identifies two strongly supported clades in Pteropyrum and its close relationship with Calligonum , confirming previous studies. Some morphologically similar species belong to different clades, which is probably due to convergent evolution and homoplasy. Leaf anatomical studies show that Atraphaxis has a multilayered mesophyll tissue, whereas Calligonum has one-layered mesophyll cells. The volume and layer number of mesophyll tissue cells decreases, whereas water storage tissue area significantly increases from Atraphaxis to Pteropyrum and Calligonum. This phenomenon confirms previous studies in other lineages with C4 salsoloid anatomy that have evolved through increasing of water storage tissue and succulence of assimilating organs. In the taxonomic part of the paper, a key to identification of accepted taxa of Pteropyrum , description of species and distribution maps are presented based on numerous herbarium specimens and our own rich collections from the field. Four new species are described based on a combination of morphology of seedlings and mature plants, pollen morphology and molecular data. A subspecific classification is suggested to show morpho-geographical variation of Pteropyrum aucheri s.l. [ABSTRACT FROM AUTHOR]