Species invasions and the changing biogeography of Australian freshwater fishes

Aim By dissolving natural physical barriers to movement, human‐mediated species introductions have dramatically reshuffled the present‐day biogeography of freshwater fishes. The present study investigates whether the antiquity of Australia's freshwater ichthyofauna has been altered by the widespread invasion of non‐indigenous fish species. Location Australia. Methods Using fish presence–absence data for historical and present‐day species pools, we quantified changes in faunal similarity among major Australian drainage divisions and among river basins of north‐eastern Australia according to the Sørensen index, and related these changes to major factors of catchment disturbance that significantly alter river processes. Results Human‐mediated fish introductions have increased faunal similarity among primary drainages by an average of 3.0% (from 17.1% to 20.1% similarity). Over three‐quarters of the pairwise changes in drainage similarity were positive, indicating a strong tendency for taxonomic homogenization caused primarily by the widespread introduction of Carassius auratus, Gambusia holbrooki, Oncorhynchus mykiss and Poecilia reticulata. Faunal homogenization was highest in drainages subjected to the greatest degree of disturbance associated with human settlement, infrastructure and change in land use. Scenarios of future species invasions and extinctions indicate the continued homogenization of Australian drainages. In contrast, highly idiosyncratic introductions of species in river basins of north‐eastern Australia have decreased fish faunal similarity by an average of 1.4%. Main conclusions We found that invasive species have significantly changed the present‐day biogeography of fish by homogenizing Australian drainages and differentiating north‐eastern river basins. Decreased faunal similarity at smaller spatial scales is a result of high historical similarity in this region and reflects the dynamic nature of the homogenization process whereby sporadic introductions of new species initially decrease faunal similarity across basins. Our study points to the importance of understanding the role of invasive species in defining patterns of present‐day biogeography and preserving the antiquity of Australia's freshwater biodiversity.     

Phylogeny of the freshwater crabs of the Western Ghats (Brachyura,Gecarcinucidae)

The Western Ghats mountain range in India is a biodiversity hotspot for a variety of organisms including a large number of endemic freshwater crab species and genera of the family Gecarcinucidae. The phylogenetic relationships of these taxa, however, have remained poorly understood. Here, we present a phylogeny that includes 90% of peninsular Indian genera based on mitochondrial 16S rRNA and nuclear histone H3 gene sequences. The subfamily Gecarcinucinae was found to be paraphyletic with members of two other subfamilies, Liotelphusinae and Parathelphusinae, nesting within. We identify a well‐supported clade consisting of north Indian species and one clade comprising mostly south Indian species that inhabit the southern ‘sky islands’ of the Western Ghats. Relationships of early diverging genera, however, were resolved with low support. This study also includes newly sampled material from an isolated mountain plateau in the northern part of the Western Ghats, representing a new species of Gubernatoriana, which we describe here as Gubernatoriana basalticola sp. n. The new species is immediately distinguished from its congeners and the related genera Ghatiana and Inglethelphusa by its carapace and cheliped morphology, which are unique among Indian freshwater crabs. This study highlights the urgent need for continued faunistic studies to assess the true diversity of gecarcinucid crabs on the Indian subcontinent, to fully understand the basal phylogenetic relationships within the freshwater crab family Gecarcinucidae, and to evaluate the conservation threat status and biogeography of the montane freshwater crabs of the Western Ghats.     

Assessing the diversity of New Zealand freshwater harpacticoid copepods (Crustacea: Copepoda) using mitochondrial DNA (COI) barcodes

Taxonomic and ecological studies of freshwater harpacticoid copepods are limited globally by the ability to easily and accurately identify specimens. Here, we test the use of the mitochondrial cytochrome c oxidase subunit I (COI) gene locus as a tool for assessing the diversity of freshwater Harpacticoida. We obtained sequences from New Zealand harpacticoid copepods, representing two families, five genera and nine species, including the non-indigenous Elaphoidella sewelli. All species were delineated by the COI gene. However, high intraspecific diversity was evident among populations of Elaphoidella bidens (>12%), and between North and South Island populations of Bryocamptus pygmaeus (>18%), potentially indicating the presence of morphologically cryptic taxa. We suggest that mitochondrial DNA (COI) sequences can provide a useful tool for the routine identification of freshwater harpacticoid copepods. Applications of these data will include assessing species diversity and biogeography as well as assisting with the detection of non-indigenous species.     

On the taxonomic status of a Dugesia species from Buenos Aires (Platyhelminthes: Turbellaria: Tricladida)

The taxonomic and distributional statuses of the freshwater planarians of South America are imperfectly understood, and a comprehensive review is sorely needed. The species known from the vicinity of Buenos Aires, Argentina, was first described by Böhmig (1902) under the name Planaria dubia Borelli, 1895. Subsequent authors (Kenk, 1930, 1974; Cazzaniga & Curino, 1987) have cast doubt on this assignation. Some have assigned it to Dugesia anceps Kenk; Hyman (1959) was inclined to regard the Buenos Aires planarian as a geographical variant of Dugesia sanchezi Hyman. A comparison of D. sanchezi from the mountainous region of central Chile with specimens from Buenos Aires confirms that the Argentinian material is a distinct species.The differences between the two species are subtle. The Argentinian specimens are distinctive in their possession of infranucleate epithelia of the atria, penis, and bursal canal, as well as in their penial structure. In both species, the epithelia of the atria and bursal canal are glandular. Those of D. sanchezi are nucleate and their secretions are cyanophilous. In the Argentinian specimens, these same epithelia are infranucleate; but while the secretion of the bursal canal is indeed cyanophilous, that of the atrium is erythrophilous. The presence, in these same specimens, of cyanophilous glands opening into the penial vesicles, and of erythrophilous glands whose secretions contribute to a viscous plug in the ejaculatory duct, suggests a difference in the physiology of copulation.It is apparent that the Argentinian specimens are distinct from D. sanchezi Hyman, and probably they represent a new species, one to be described in detail elsewhere. In any case, Hyman's (1959) suggestion that D. sanchezi occurs near Buenos Aires is mistaken; so also is Cazzaniga's & Curino's (1987) identification of specimens from Buenos Aires as D. anceps.     

Clarifying an ambiguous evolutionary history: range‐wide phylogeography of an Australian freshwater fish,the golden perch (Macquaria ambigua)

Aim We conducted a range‐wide phylogeographic study of a common Australian freshwater fish, the golden perch (Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins. Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] of eastern Australia. Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation‐with‐migration model simulations. Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (Φ_ST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene. Main conclusions Investigation of the range‐wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios.     

Molecular analyses of turf algae reveal a new species and an undetected introduction in the Pterosiphonieae (Rhodomelaceae,Rhodophyta)

Introduced seaweeds and undescribed species often remain undetected because marine regional floras are as yet poorly understood. DNA sequencing facilitates their detection, but databases are incomplete, so their improvement will continue to lead the discovery of these species. Here we aim to clarify the taxonomy of two turf-forming red algal Australian species that morphologically resemble the European Aphanocladia stichidiosa. We also aim to elucidate whether either of these species could have been introduced in Europe or Australia. We studied their morphology, analyzed 17 rbcL sequences of European and Australian specimens, examined their generic assignment using a phylogeny based on 24 plastid genomes, and investigated their biogeography using a taxon-rich phylogeny including 52 rbcL sequences of species in the Pterosiphonieae. The rbcL sequences of one of the Australian species were identical to A. stichidiosa from Europe, considerably expanding its known distribution. Unexpectedly, our phylogenetic analyses resolved this species in the Lophurella clade rather than in Aphanocladia and the new combination L. stichidiosa is proposed. The other Australian species is described as L. pseudocorticata sp. nov. Although L. stichidiosa was originally described in the Mediterranean ca. 70 years ago, our phylogenetic analyses placed it in a lineage restricted to the southern hemisphere, showing that it is native to Australia and introduced to Europe. This study confirms that further work using molecular tools is needed to characterize seaweed diversity, especially among the poorly explored algal turfs, and showcases the usefulness of phylogenetic approaches to uncover introduced species and to determine their native ranges.     

Chromosome bands in freshwater triclads

Four species of Triclads belonging to three families, Dugesia polychroa and Dugesia mediterranea (Dugesiidae), Planaria torva (Planariidae) and Dendrocoelum lacteum (Dendrocoelidae) were studied for chromosome banding: C-banding for all the species, ASG banding for Dugesia polychroa and G-banding for Dugesia polychroa and Dugesia mediterranea. C-banding results for Dugesia lugubris-polychroa group suggest a high level of heterochromatin evolution in the group. Small bands strictly limited to the centromeric region were seen in Dugusia lugubris and this pattern is similar to the patterns of some species belonging to other families, notably Planaria torva and Dendrocoelum lacteum. This could be considered a primitive character. In contrast numerous heterochromatin bands which are useful to characterize the different karyotypes were seen in Dugesia polychroa and Dugesia mediterranea. Our data suggest that heterochromatin is important in freshwater triclad speciation.     

Cryptic species within the Chydorus sphaericus species complex (Crustacea: Cladocera) revealed by molecular markers and sexual stage morphology

The cosmopolitanism paradigm in the biogeography of freshwater invertebrates is currently being replaced by non-cosmopolitanism or continental endemism. Benthic water fleas (Cladocera) from the family Chydoridae were the first group of freshwater invertebrates for which non-cosmopolitanism and cryptic diversity was substantiated by morphological studies. Yet, little is known about genetic differentiation and evolutionary history of chydorid species complexes. Here we present the first analysis of the genetic versus morphological differentiation in a benthic cladoceran species complex—Chydorus sphaericus s. str. using sequence variation in a nuclear (ribosomal internal transcribed spacer 2, ITS-2) and a mitochondrial (cytochrome c oxidase subunit I, COI) genes in 50 Holarctic localities. We tested for continental endemism and cryptic diversity predicted by previous morphological studies. We found evidence for the presence of at least seven putative regional species in the Holarctic, at least three of them being distributed beyond a single continent. While the molecular and sexual stage characters showed general concordance on species lineages, parthenogenetic female characters lacked resolution or were unassociated with molecular lineages. We conclude that cryptic regional lineages of benthic cladocerans are apparent and that the sexual stages represent the most informative morphological source of species characters for this environmental indicator group.     

Gladioferens Henry (Copepoda: Calanoida) discovered in Antarctica: G. antarcticus sp. nov. described from a lake in the Bunger Hills

A new species of Gladioferens is described from a freshwater lake in the Bunger Hills, Greater Antarctica. A key to the six species of Gladioferens is provided for both sexes. Most species of the subgenus containing G. antarcticus sp. nov. are remarkable in possessing asymmetries in the second legs (male) and fourth legs (female). This suggests that the mating behaviour of these species may be radically different from that in most heterarthrandrian calanoids and calls for further study. However, G. antarcticus is more primitive than its consubgeners in having, in the male, symmetrical second legs and 3-segmented endopods in the fifth legs. The genus shows a highly disjunct distribution (Australia, New Zealand and Bunger Hills) and its biogeography is now of outstanding interest.     

Renal mucous production in Australian freshwater plotosid and ariid catfishes

This study reports the presence of large mucous cells lining the large renal collecting ducts and opisthonephric ducts of the Australian freshwater catfishes Tandanus tandanus and Tandanus tropicanus. Histologic examination of the renal tissue from four other species of Australian freshwater catfishes suggests that this feature is unique to the two species of Tandanus studied. The potential functions of renal mucous secretion in T. tandanus and T. tropicanus are discussed.     

Hidden diversity in the freshwater planktonic diatom Asterionella formosa

Many freshwater and marine algal species are described as having cosmopolitan distributions. Whether these widely distributed morphologically similar algae also share a similar gene pool remains often unclear. In the context of island biogeography theory, stronger spatial isolation deemed typical of freshwater lakes should restrict gene flow and lead to higher genetic differentiation among lakes. Using nine microsatellite loci, we investigate the genetic diversity of a widely distributed freshwater planktonic diatom, Asterionella formosa, across different lakes in Switzerland and the Netherlands. We applied a hierarchical spatial sampling design to determine the geographical scale at which populations are structured. A subset of the isolates was additionally analysed using amplified fragment length polymorphism (AFLP) markers. Our results revealed complex and unexpected population structure in A. formosa with evidence for both restricted and moderate to high gene flow at the same time. Different genetic markers (microsatellites and AFLPs) analysed with a variety of multivariate methods consistently revealed that genetic differentiation within lakes was much stronger than among lakes, indicating the presence of cryptic species within A. formosa. We conclude that the hidden diversity found in this study is expected to have implications for the further use of A. formosa in biogeographical, conservation and ecological studies. Further research using species‐level phylogenetic markers is necessary to place the observed differentiation in an evolutionary context of speciation.     

Lack of phylogeographic structure in three widespread Australian birds reinforces emerging challenges in Australian historical biogeography

Aims Building on molecular studies of widespread Australian vertebrates, we tested whether each of three widespread Australian bird species, namely the singing honeyeater, Lichenostomus virescens, spiny‐cheeked honeyeater, Acanthagenys rufogularis (Passeriformes: Meliphagidae), and black‐faced woodswallow, Artamus cinereus (Passeriformes: Artamidae), has undergone a recent (Pleistocene) range expansion across the Australian continent. We related the findings to the presence or absence of geographic variation in each species’ external phenotype and whether historical or non‐historical factors have been involved in generating variation. Methods A total of 92 specimens of the three species were collected from, as far as possible, the same localities across Australia. They were sampled for mitochondrial DNA (mtDNA) diversity in the 1041 base pairs of the ND2 gene, and these data were analysed with nucleotide diversity statistics, unrooted networks, nested clade analysis, and tests of range expansion or stability. Results Range expansions could not be rejected in any of the species in our study. Each had low, geographically unstructured nucleotide diversity. Patterns of geographic variation in the singing honeyeater's and, to a lesser extent, the black‐faced woodswallow's external phenotypes are not correlated with mtDNA diversity in ND2. Main conclusions Our study adds to the increasing number of data sets suggesting the apparent prevalence of Pleistocene population expansions in widespread Australian birds. Furthermore, it shows that observable geographic structure may evolve very quickly, in response either to environmental gradients or to historical factors that operated too recently to be detected by ND2 sequences (e.g. in the singing honeyeater). Conversely, we have shown that a species that has had a recent population expansion need not necessarily be geographically invariant. To understand fully the interplay between vicariance and dispersal in the history of widespread Australian arid‐zone birds, or between the historical and non‐historical origins of their differentiation, carefully conducted case‐by‐case molecular studies will be necessary. Only then will biogeographical patterns and the processes that led to them emerge. Study of the historical biogeography and the more recent population history of Australian arid‐zone birds has reached a point where mtDNA‐based studies, while still informative and contributing to a growing data base of such work, should be complemented with data from multiple, rapidly evolving nuclear loci.     

Diversity and abundance of nematode-trapping fungi from decaying litter in terrestrial, freshwater and mangrove habitats

Nematode-trapping fungi are ubiquitous in terrestrial habitats in dung, soils, litter and woody debris and they also occur in freshwater, but only one species has been found in marine habitats. The purpose of this study was therefore to investigate whether nematode-trapping fungi occurred in mangrove habitats. To achieve this we assessed the diversity of nematode-trapping fungi on decaying litter from mangroves, freshwater and terrestrial habitats (22 sites) in Hong Kong. Composite samples (n = 1,320) of decaying litter (wood and leaves) were examined and a total of 31 species of nematode-trapping fungi belonging to four genera, Arthrobotrys, Monacrosporium, and Dactylella were recorded. Twenty-nine species reported in this study are new records for Hong Kong and 16 species are new records from mangrove habitats worldwide. Nematode trapping fungi are therefore present in marine environments. Commonly encountered taxa were Arthrobotrys oligospora and Monacrosporium thaumasium which are abundant in all habitats. A. oligospora, M. thaumasium and Arthrobotrys musiformis were frequent (F > 10%). Twenty-six species were rare (0.16–9.32%). Species richness and diversity was higher in terrestrial than in freshwater and mangrove habitats (ANOVA, P < 0.001). A higher mean diversity was observed on decaying leaves as compared to decaying wood in all habitats (P < 0.001). Based on Shannon diversity index, it was also observed that taxa characterized by adhesive nets were more frequent in all habitats. This can be explained by the fact that these taxa may have a better competitive saprotrophic ability which would allow them to compete favourably in nutrient limited environments. Abiotic factors that could be linked to differences in species diversity between decaying wood and leaves are also discussed.     

New World Heterotermes (Isoptera,Rhinotermitidae): molecular phylogeny,biogeography and description of a new species

Heterotermes Froggatt is a subterranean termite genus consisting of 30 living described species worldwide, with nine occurring in the New World. Herein we provide a molecular phylogeny, using both mitochondrial and nuclear markers, of all New World species of Heterotermes, including biogeographical analysis, and describe a new species from Paraguay and Bolivia, based on morphological and molecular evidence. Our analysis recovered the New World species as paraphyletic to a monophyletic Australian clade. Within this New World + Australian clade, two monophyletic major groups were formed c. 28 Ma: the aureus- and tenuis-groups. The aureus-group has a disjunct and broad distribution consisting of two clades. The first clade extends into the Nearctic region and a second is composed of a branch in the Caatinga and Cerrado biomes (H. sulcatus Mathews) and a branch in the Chacoan biome (a new species, Heterotermes lauralinearum Carrijo sp.n. ). The tenuis-group is composed of four broadly distributed Neotropical species and the Australian clade. A single dispersion event from South America to Australia probably occurred between 13 and 24 Ma. Heterotermes crinitus Emerson was the first to diverge, being sister group of all other species in the tenuis-group, followed by Heterotermes assu Constantino. An analysis of the historical biogeography of Heterotermes suggests that jump dispersal was the most important cladogenetic process for the genus. This study is the most comprehensive phylogeny of Heterotermes and contributes to the understanding of termite evolution and geographic distribution in the New World, complementing recent studies focused on worldwide patterns. This published work has been registered on Zoobank, http://zoobank.org/urn:lsid:zoobank.org:pub:8951A29B-8B69-4CD5-B9DF-2C70D4628D97 .     

Oceanic island biogeography through the lens of the general dynamic model: assessment and prospect

The general dynamic model of oceanic island biogeography (GDM) has added a new dimension to theoretical island biogeography in recognizing that geological processes are key drivers of the evolutionary processes of diversification and extinction within remote islands. It provides a dynamic and essentially non‐equilibrium framework generating novel predictions for emergent diversity properties of oceanic islands and archipelagos. Its publication in 2008 coincided with, and spurred on, renewed attention to the dynamics of remote islands. We review progress, both in testing the GDM's predictions and in developing and enhancing ecological–evolutionary understanding of oceanic island systems through the lens of the GDM. In particular, we focus on four main themes: (i) macroecological tests using a space‐for‐time rationale; (ii) extensions of theory to islands following different patterns of ontogeny; (iii) the implications of GDM dynamics for lineage diversification and trait evolution; and (iv) the potential for downscaling GDM dynamics to local‐scale ecological patterns and processes within islands. We also consider the implications of the GDM for understanding patterns of non‐native species diversity. We demonstrate the vitality of the field of island biogeography by identifying a range of potentially productive lines for future research.     

Rodent louse diversity,phylogeny, and cospeciation in the Manu Biosphere Reserve,Peru

We investigated the diversity, cophylogenetic relationships, and biogeography of hoplopleurid sucking lice (Phthiraptera: Anoplura) parasitizing rodents (Muridae: Sigmodontinae) in the Manu National Park and Biosphere Reserve. Our morphological and molecular studies reveal that 15 distinct louse species parasitize 19 rodent species. Three of these louse species are new to science, and all but two of the host associations were previously unknown. We find that hoplopleurid lice in South America parasitize multiple host species across a large geographic area, and that Peru represents a new geographic locality for almost all the louse species collected in the present study. Phylogenetic analyses of mitochondrial and nuclear data reveal that the louse family Hoplopleuridae and the genera Hoplopleura and Pterophthirus are not monophyletic, and lice do not appear to group by host tribe, collecting locality, or collection elevation. The lack of monophyly for these apparently natural groups (taxonomic, locality, and elevation) indicates that host switching with or without parasite speciation may be prevalent among hoplopleurid lice. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 598–610.     

Marine island biogeography. Response to comment on ‘Island biogeography: patterns of marine shallow‐water organisms’

In this response we have incorporated data on gastropod and seaweed biodiversity referred to by Ávila et al. (2016, Journal of Biogeography, doi: 10.1111/jbi.12816 ) to allow an updated analysis on marine shallow‐water biogeography patterns. When compared to the biogeography patterns reported in Hachich et al. (2015, Journal of Biogeography, 42 , 1871–1882), we find (1) no differences in the patterns originally reported for reef fish or seaweeds, (2) minor differences in gastropod species–area and species–age patterns and (3) a significant difference for the gastropod species‐isolation pattern. In our original work, we reported that there was limited evidence that gastropod species richness was influenced by island isolation; however, our new analysis reveals a power‐model relationship between these variables. Thus, we are now able to conclude that gastropod species diversity, whose dispersal capacity is intermediate between seaweeds (lowest) and reef fish (highest), is also influenced by island isolation.     

Freshwater mussel (Mollusca: Bivalvia: Unionoida) richness and endemism in the ecoregions of Africa and Madagascar based on comprehensive museum sampling

The objective of this study was to assess freshwater mussel (Mollusca: Bivalvia: Unionoida) species distributions among the freshwater ecoregions of Africa and Madagascar to discover areas of high richness and endemism. These are among the top criteria for identifying biodiversity hotspots and establishing conservation priorities. Distributions were determined from museum specimens in 17 collections. In total, 5,612 records for 87 unionoid species could each be assigned to one of 90 freshwater ecoregions. The majority of species (55%) are known from only one (34 spp.) or two (14) ecoregions. Only three are known from more than 20 ecoregions: Etheria elliptica (38 ecoregions), Chambardia wahlbergi (25), and Mutela rostrata (21). The most species-rich ecoregions are Lake Victoria Basin (17 spp.), Upper Nile (16), Upper Congo (14), Senegal–Gambia (13), and Sudanic Congo–Oubangi (13). Those with the most endemic species are Lake Tanganyika (8 spp.), Lake Victoria Basin (6), Bangweulu–Mweru (4), and Lake Malawi (3). Twenty-five ecoregions have no known freshwater mussels. These patterns are significantly correlated with fish and general freshwater mollusk richness. Unionoid richness also varies significantly among major habitat types. These patterns are relevant to biogeography and conservation and indicate areas in need of further research. We argue that freshwater mussels are valuable as focal species for conservation assessments, and they themselves merit management consideration for their ecosystem functions and distributions in imperiled habitats. It is recommended that field surveys be conducted to determine the current status of species in all areas of Africa and Madagascar.     

Complex phylogeographic patterns in the freshwater alga Synura provide new insights into ubiquity vs. endemism in microbial eukaryotes

The global distribution, abundance, and diversity of microscopic freshwater algae demonstrate an ability to overcome significant barriers such as dry land and oceans by exploiting a range of biotic and abiotic colonization vectors. If these vectors are considered unlimited and colonization occurs in proportion to population size, then globally ubiquitous distributions are predicted to arise. This model contrasts with observations that many freshwater microalgal taxa possess true biogeographies. Here, using a concatenated multigene data set, we study the phylogeography of the freshwater heterokont alga Synura petersenii sensu lato. Our results suggest that this Synura morphotaxon contains both cosmopolitan and regionally endemic cryptic species, co‐occurring in some cases, and masked by a common ultrastructural morphology. Phylogenies based on both proteins (seven protein‐coding plastid and mitochondrial genes) and DNA (nine genes including ITS and 18S rDNA) reveal pronounced biogeographic delineations within phylotypes of this cryptic species complex while retaining one clade that is globally distributed. Relaxed molecular clock calculations, constrained by fossil records, suggest that the genus Synura is considerably older than currently proposed. The availability of tectonically relevant geological time (10⁷–10⁸ years) has enabled the development of the observed, complex biogeographic patterns. Our comprehensive analysis of freshwater algal biogeography suggests that neither ubiquity nor endemism wholly explains global patterns of microbial eukaryote distribution and that processes of dispersal remain poorly understood.