High genetic differentiation among populations of the small cavy Microcavia australis occupying different habitats

The small cavy Microcavia australis, a social and fossorial rodent, inhabits a large distribution range in South American arid zones. The species is versatile in coping with the seasonal and spatial variability typical of these environments through changes in morphology, physiology, and behavior. In order to explore whether phenotypic variations are related to the evolutionary history of the species, we analyzed the levels of genetic variability and divergence among four populations that differ in climate and habitat characteristics, two belonging to highlands and the other two from lowlands. We sequenced the mitochondrial control region and used the Inter Simple Sequence Repeats technique to study variability in the noncoding nuclear genome. Results from both genetic markers were consistent. Variability levels were high for all populations, and even higher for lowland ones. Pairwise genetic differentiation varied greatly, all comparisons being statistically significant except for the two highland populations. Seventeen haplotypes were detected which displayed three clear lineages: two corresponding to each lowland population and one to those in the highlands. Levels of genetic differentiation between population pairs varied widely. Haplotypes showed a mean sequence divergence of 1.4% between lowland populations and 0.2% between highland ones, whereas divergence was around 9% when populations from different altitudes were compared. Results from BEAST analysis support extant hypotheses suggesting that lowland forms are clearly older than the highland group. The deep genetic divergence between lineages poses the need to search for new evidence for properly defining the taxonomic status of divergent populations of M. australis.     

Genetic divergence and speciation in lowland and montane peruvian poison frogs

Amazonia is famous for high biodiversity, and the highlands of the transition zone between the Andes and the lowlands of the Amazon basin show particularly high species diversity. Hypotheses proposed to explain the high levels of diversity in the highlands include repeated parapatric speciation across ecological gradients spanning the transition zone, repeated allopatric speciation across geographic barriers between the highlands and lowlands, divergence across geographic barriers within the transition zone, and simple lineage accumulation over long periods of time. In this study, we investigated patterns of divergence in frogs of the genus Epipedobates (family Dendrobatidae) using phylogenetic and biogeographic analyses of divergence in mitochondrial DNA (1778 aligned positions from genes encoding cyt b, 12S and 16S rRNA for 60 Epipedobates and 11 outgroup specimens) and coloration (measured for 18 specimens representing nine species in Epipedobates). The majority of phenotypic and species diversity in the poison frog genus Epipedobates occurs in the transition zone, although two morphologically conserved members of the genus are distributed across the lowlands of the Amazon basin. Phylogenetic analysis reveals that there is a single highland clade derived from an ancestral colonization event in northern Peru by a population of lowland ancestry. Epipedobates trivittatus, a widespread Amazonian species, is a member of the highland clade that reinvaded the lowlands. Comparative analyses of divergence in coloration and mtDNA reveals that divergence in coloration among populations and species in the highlands has been accelerated relative to the lowlands. This suggests a role for selection in the divergence of coloration among populations and species.     

Speciation and evolution of eco‐climatic ranges in the intertropical African dung beetle genus,Diastellopalpus van Lansberge

We investigate how late Cenozoic orogenics and climatic change might have influenced the history of taxon diversification and current species ranges of an endemic, Afrotropical, insect genus. Diastellopalpus van Lansberge is a near basally‐derived taxon in the dung beetle tribe Onthophagini (Coleoptera: Scarabaeidae: Scarabaeinae) that has diversified into 32 known species primarily centred on intertropical forests. Basal dichotomies in both published and re‐analysed phylogenies divide the species into clades that are geographically centred either to the east or west of the south‐east highlands that underwent uplift from the Miocene. There is broad climatic overlap between many of the species but clear separation along a minimum spanning tree in ordinal space where they are divided into taxa with either lowland or highland centres of distribution. Observed spatial distributions of six defined species groups mostly differ from predicted climatic ranges, presumably as a result of historical constraints on species dispersal. A trend from dominance of montane or wet lowland forest associations in species lineages derived from more basal nodes (Groups A–C) to dominance of drier upland forest and moist woodland associations in species lineages derived from a more terminal node (Groups D–F) is perhaps linked to the stepped trend to cooler, dryer climate in the late Cenozoic. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 407–423.     

Evaluating condition-specific and asymmetric competition in a species-distribution context

Mechanisms resulting in parapatric distributions of closely related taxa have long interested ecologists. If two species are distributed across an environmental gradient, and differ in their ability to cope with environmental conditions, the outcome of competitive interactions may be dependent on prevailing abiotic conditions. Two closely related species of poison frogs in north–central Peru were observed to occupy parapatric distributions across an elevation gradient. Ameerega bassleri is a highland endemic restricted to a small region of Peru, and A. trivittata is distributed throughout lowland Amazonia. The goal of this study was to examine the effect of an abiotic factor (elevation) on two biotic factors (intraspecific and interspecific competition), by measuring growth and survival in the larvae of A. trivittata and A. bassleri . Using mesocosm experiments arranged in a fractional factorial design, we found that (1) A. bassleri had a strong negative effect on the growth and survival of A. trivittata regardless of elevation, (2) A. trivittata had no effect on the growth of A. bassleri at either elevation, but did appear to reduce the survival of A. bassleri more strongly in the lowlands than highlands, (3) lowland conditions uniformly reduced survival in all treatments and in both species, and (4) competition was strongly asymmetric between A. bassleri and A. trivittata . We conclude that the perceived low density of A. trivittata in highland sites may be influenced by the presence of A. bassleri, but the lower limit to the distribution of A. bassleri cannot be explained by competition with A. trivittata and may be due to physiological constraints imposed by lowland conditions.     

Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia

The frog genus Leptopelis is composed of ~50 species that occur across sub‐Saharan Africa. The majority of these frogs are typically arboreal; however, a few species have evolved a fossorial lifestyle. Most species inhabit lowland forests, but a few species have adapted to high elevations. Five species of Leptopelis occupy the Ethiopian highlands and provide a good opportunity to study the evolutionary transition from an arboreal to a fossorial lifestyle, as well as the diversification in this biodiversity hot spot. We sequenced 14 nuclear and three mitochondrial genes, and generated thousands of SNPs from ddRAD sequencing to study the evolutionary relationships of Ethiopian Leptopelis. The five species of highland Leptopelis form a monophyletic group, which diversified during the late Miocene and Pliocene. We found strong population structure in the fossorial species L. gramineus, with levels of genetic differentiation between populations similar to those found between arboreal species. This could indicate that L. gramineus is a complex of cryptic species. We propose that after the original colonization of the Ethiopian highlands by the ancestor of the L. gramineus group, episodes of vicariance fragmented the ancestral populations of this group. We also report the re‐evolution of arboreality in L. susanae, which evolved from a fossorial ancestor, a rare ecological switch in frogs that had previously been reported only once.     

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.     

Lowland panmixia versus highland disjunction: genetic and bioacoustic differentiation in two species of East African White-eye birds

East-African mountain forest species often occur in small and isolated populations, whereas species inhabiting the dry lowland savannahs exist in large and interconnected population networks. Taxa with closely related highland and lowland species, such as the East-African White-eye birds, allow testing for the potential effects of the two contrasting distribution patterns, mountain disjunction versus lowland panmixia. In this study, we compare the population genetic and bioacoustic differentiation of two representatives of the genus Zosterops: Zosterops poliogaster is exclusively found in forests at higher elevations; in comparison, Zosterops abyssinicus, only occurs in the dry and warm lowland savannahs. Both species were analysed across a similar geographical scale. Population genetic differentiation was inferred using the same set of 15 polymorphic microsatellite loci for both species. In addition, we quantitatively analyzed bioacoustic traits. Both data sets indicate a strong population differentiation among populations of the highland species, but an absence of differentiation in the lowland species. In addition, the lowland Z. abyssinicus was characterised by a twofold higher genetic diversity than detected for the highland Z. poliogaster. These two contrasting intraspecific population structures may reflect the opposite ecology and distribution of these species: the strong population isolation of Z. poliogaster resulting from long-term restriction to the cool and moist mountain forests at higher elevations has led to strong differentiation among local populations and resulted in a comparatively low level of intraspecific variability. In contrast, population panmixia in the lowland Z. abyssinicus provides a high level of gene flow allowing the maintenance of high genetic diversity and avoiding strong population structuring. These findings need to be considered when planning conservation actions.     

Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography

Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.     

Altitudinal species turnover in southern Tanzania shown by anurans: Some zoogeographical considerations

A transect was used to investigate the pattern of altitudinal species turnover shown by the rich fauna of frogs and toads in southeastern Tanzania, and to compare the pattern with those shown by transects taken further south. The transect, taken from the Udzungwa range to the southeastern coast, was divided into 50 m intervals. As with the southern transects, there appears to be a major grouping into lowland and highland sets, with opposing and overlapping subtraction margins that form a replacement‐transition zone. A distributionally complex assemblage of species occurs in this zone. When a similarity value (the Dice‐S?rensen index, expressed as a percentage) taken between the montane ridge and lowland faunas was compared with those of the southern transects, a markedly higher species turnover (low similarity value) is shown in Tanzania. Both lowland and highland faunas have more species than equivalent faunas to the south; the highland fauna is particularly rich in genera not known to occur further south. Yet overall, the pattern of altitudinal turnover shown in the Tanzanian transect is in agreement with the pattern shown in the southern transects. The transects discussed in this paper, combined with other evidence, suggest a need for re‐evaluating the common practice of including all sub‐Saharan Africa in a single so‐called Afrotropical Region.     

Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography

Aim  We used inferences of phylogenetic relationships and divergence times for three lineages of highland pitvipers to identify broad-scale historical events that have shaped the evolutionary history of Middle American highland taxa, and to test previous hypotheses of Neotropical speciation.
Location  Middle America (Central America and Mexico).
Methods  We used 2306 base pairs of mitochondrial gene sequences from 178 individuals to estimate the phylogeny and divergence times of New World pitviper lineages, focusing on three genera ( Atropoides , Bothriechis and Cerrophidion ) that are broadly co-distributed across Middle American highlands.
Results  We found strong correspondence across three highland lineages for temporally and geographically coincident divergences in the Miocene and Pliocene, and further identified widespread within-species divergences across multiple lineages that occurred in the early–middle Pleistocene.
Main conclusions  Available data suggest that there were at least three major historical events in Middle America that had broad impacts on species divergence and lineage diversification among highland taxa. In addition, we find widespread within-species genetic structure that may be attributable to the climatic changes that affected gene flow among highland taxa during the middle–late Pleistocene.     

Mitochondrial phylogeographies of five widespread Eurasian bird species

Five species of Eurasian birds displayed a range of mitochondrial DNA phylogeographic structures, including a single widespread lineage (common sandpiper), two geographically unsorted and closely related lineages (long-tailed tit), three partially overlapping closely related lineages (reed bunting), and two divergent geographically isolated lineages that rival species distinction (red-breasted flycatcher and skylark). Only the red-breasted flycatcher and the skylark displayed congruent phylogeographic structures. These five species represent different stages of diversification and speciation. There was little evidence that natural selection had influenced mitochondrial NADH dehydrogenase subunit 2 (ND2) sequences. In several instances, population growth was hypothesized, based on haplotype distributions within populations.     

The Lethal Fungus Batrachochytrium dendrobatidis Is Present in Lowland Tropical Forests of Far Eastern Panamá

The fungal disease chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), is one of the main causes of amphibian population declines and extinctions all over the world. In the Neotropics, this fungal disease has caused catastrophic declines in the highlands as it has spread throughout Central America down to Panamá. In this study, we determined the prevalence and intensity of Bd infection in three species of frogs in one highland and four lowland tropical forests, including two lowland regions in eastern Panamá in which the pathogen had not been detected previously. Bd was present in all the sites sampled with a prevalence ranging from 15–34%, similar to other Neotropical lowland sites. The intensity of Bd infection on individual frogs was low, ranging from average values of 0.11–24 zoospore equivalents per site. Our work indicates that Bd is present in anuran communities in lowland Panamá, including the Darién province, and that the intensity of the infection may vary among species from different habitats and with different life histories. The population-level consequences of Bd infection in amphibian communities from the lowlands remain to be determined. Detailed studies of amphibian species from the lowlands will be essential to determine the reason why these species are persisting despite the presence of the pathogen.     

Intricate evolutionary histories in montane species: a phylogenetic window into craniodental discrimination in the Peromyscus mexicanus species group (Mammalia: Rodentia: Cricetidae)

Mountain‐associated species, which exhibit allopatric distributions associated with elevation, endemisms and complex evolutionary histories, pose challenging evolutionary scenarios in which to discern the diversification of species. The Peromyscus mexicanus mice group, distributed along mountains in southern Mexico and Central America, is morphometrically variable, a key rationale for the ongoing controversy regarding its species delimitation. Based on the recognized 15 mitochondrial lineages for the group, we analysed external and craniodental morphometric variables to test whether lineages can be differentiated morphometrically and allow for the delimitation of species. We also aimed to test the prediction that the phylogenetic structure of the morphometric data is concordant with that of the molecular information. Based on 19 craniodental measurements from 521 specimens, multivariate and discriminant analyses showed that lineages are morphometrically discernible, representing distinct phenotypes, and that overall size and mandible measurements are significant features that discriminate lineages, supporting hypotheses about differences in feeding habits between species. Also, a pattern of increasing size with elevation was observed, further supported by specific morphological differences exhibited between highland and lowland lineages inhabiting the same mountain. Our results demonstrate that P. mexicanus is both genetically and morphometrically variable, where most highland montane species are differentiated from lowland species; also, a significant correlation between mitochondrial and morphometric information is indicative of phenetic concordance, altogether in agreement with a recent taxonomic proposal for the group. We suggest that the group's intricate diversification responds to ecological diversification and adaptation to a variety of mountain habitats and Pleistocene biogeographic climatic dynamics.     

MOLECULAR AND REPRODUCTIVE CHARACTERIZATION OF SIBLING SPECIES IN THE EUROPEAN EARWIG (FORFICULA AURICULARIA)

The European earwig (Forficula auricularia) was formerly thought to present a mosaic of populations differing in their reproductive biology. We show that it is comprised of two as yet unrecognized sibling species. The molecular divergence between the two species, for a 627-bp amplified fragment overlapping the COI and COII mitochondrial loci, is six times larger than intraspecific variation. A species with two clutches a year lives predominantly in lowland and oceanic European habitats. A species with one clutch a year—except in the Mediterranean area where it has two clutches—lives predominantly in highland and continental European habitats. They both invaded North America during the 20th century, respectively, from the west and the east coasts, with no apparent mixing of their populations. The two species can occur in sympatry in Europe and are reproductively isolated by nearly complete failure to produce F₁ hybrids.     

Evolution along the Great Rift Valley: phenotypic and genetic differentiation of East African white‐eyes (Aves,Zosteropidae)

The moist and cool cloud forests of East Africa represent a network of isolated habitats that are separated by dry and warm lowland savannah, offering an opportunity to investigate how strikingly different selective regimes affect species diversification. Here, we used the passerine genus Zosterops (white‐eyes) from this region as our model system. Species of the genus occur in contrasting distribution settings, with geographical mountain isolation driving diversification, and savannah interconnectivity preventing differentiation. We analyze (1) patterns of phenotypic and genetic differentiation in high‐ and lowland species (different distribution settings), (2) investigate the potential effects of natural selection and temporal and spatial isolation (evolutionary drivers), and (3) critically review the taxonomy of this species complex. We found strong phenotypic and genetic differentiation among and within the three focal species, both in the highland species complex and in the lowland taxa. Altitude was a stronger predictor of phenotypic patterns than the current taxonomic classification. We found longitudinal and latitudinal phenotypic gradients for all three species. Furthermore, wing length and body weight were significantly correlated with altitude and habitat type in the highland species Z. poliogaster. Genetic and phenotypic divergence showed contrasting inter‐ and intraspecific structures. We suggest that the evolution of phenotypic characters is mainly driven by natural selection due to differences in the two macro‐habitats, cloud forest and savannah. In contrast, patterns of neutral genetic variation appear to be rather driven by geographical isolation of the respective mountain massifs. Populations of the Z. poliogaster complex, as well as Z. senegalensis and Z. abyssinicus, are not monophyletic based on microsatellite data and have higher levels of intraspecific differentiation compared to the currently accepted species.     

Meller's duck: A threatened species receives recognition at last

Wetland areas of Madagascar, increasingly threatened by extensive habitat modification, contain many little known endemic species. One of these species, Meller's duck (Anas melleri), is restricted to the eastern slope of the central highlands but for many years was just considered a recent island isolate of the widespread common mallard (A. platyrhynchos) and, therefore, not worthy of protection. Phylogenetic analysis, based on mitochondrial d-loop DNA sequences, indicates that Meller's duck is distinct from the mallard and from its nearest geographical congener, the yellow-billed duck (A. undulata) and may have evolved from a non-dimorphic ancestor, the African black duck (A. sparsa). A decline in numbers of the Near-Threatened Meller's duck highlights the need for adequate protection for Madagascar's wetlands.     

Extreme population subdivision throughout a continuous range: phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America

Low-vagility species with deep evolutionary histories are key to our understanding of the biogeographical history of geologically complex areas, such as the west coast of North America. We present a detailed study of the phylogeography of the salamander Batrachoseps attenuatus (Caudata: Plethodontidae) using sequences of the mitochondrial gene cob from 178 individuals sampled from throughout the species' range. Sequences of three other mitochondrial genes (16S, cox1, nad4) and a nuclear gene (RAG-1) were used to investigate the deeper evolutionary history of the species. We found high levels of genetic diversity and deep divergences within a mostly continuous distribution, with five genetically well-differentiated and geographically structured mitochondrial DNA clades. Significant association between geographical and genetic distances within these clades suggests demographic stability, whereas Fu's FS tests suggest demographic expansions in three of them. Mantel tests identify two biogeographical barriers, the San Andreas Fault and the Sacramento-San Joaquin Delta, as important in the diversification of lineages. The timing of the main splitting events between intraspecific lineages was estimated by applying relaxed molecular clock methods combining several mutation rates and a fossil calibration. The earliest splitting events are old (Pliocene/Miocene), with more recent (Pleistocene) subdivisions in some clades. Disjunct populations distributed along the western foothills of the Sierra Nevada colonized this area relatively recently from a single refugium east of San Francisco Bay. The combination of fine-scale, comprehensive sampling with phylogenetic, historical demographic and hypothesis-based tests allowed delineation of a complex biogeographical scenario with general implications for the study of codistributed taxa.     

Seasonal effects and fine‐scale population dynamics of Aedes taeniorhynchus,a major disease vector in the Galapagos Islands

Characterization of the fine‐scale population dynamics of the mosquito Aedes taeniorhynchus is needed to improve our understanding of its role as a disease vector in the Galapagos Islands. We used microsatellite data to assess the genetic structure of coastal and highland mosquito populations and patterns of gene flow between the two habitats through time on Santa Cruz Island. In addition, we assessed possible associations of mosquito abundance and genetic diversity with environmental variables. The coastal and highland mosquito populations were highly differentiated from each other all year round, with some gene flow detected only during periods of increased precipitation. The results support the hypothesis that selection arising from ecological differences between habitats is driving adaptation and divergence in A. taeniorhynchus, and maintaining long‐term genetic differentiation of the populations against gene flow. The highland and lowland populations may constitute an example of incipient speciation in progress. Highland populations were characterized by lower observed heterozygosity and allelic richness, suggesting a founder effect and/or lower breeding site availability in the highlands. A lack of reduction in genetic diversity over time in highland populations suggests that they survive dry periods as dormant eggs. Association between mosquito abundance and precipitation was strong in the highlands, whereas tide height was the main factor affecting mosquito abundance on the coast. Our findings suggests differences in the infection dynamics of mosquito‐borne parasites in the highlands compared to the coast, and a higher risk of mosquito‐driven disease spread across these habitats during periods of increased precipitation.     

An integrative assessment of the taxonomic status of putative hybrid leopard frogs (Anura: Ranidae) from the Chortís Highlands of Central America,with description of a new species

Integrative taxonomy seeks to approach the complex topic of species diagnosis using independent, complementary lines of evidence. Despite their ubiquity throughout North and Central America, taxonomy of the American leopard frogs (Anura: Ranidae: Rana: subgenus Pantherana) remains largely unresolved, and this is arguably nowhere truer than in the Central American country of Honduras, where there are two nominal species, the taxonomy of which remains unresolved. Leopard frogs from several mountainous areas along the continental divide in Honduras have previously been considered putative hybrids between Rana brownorum and R. cf. forreri, as opposed to two alternate hypotheses: one that they represent a high-altitude eco-morph of a single widespread species that included both lowland forms, or a second that there is an undescribed highland species distinct from either of the recognized lowland forms. We examine this set of hypotheses using three independent lines of evidence. First, we used species distribution modelling to examine potential geographic isolation of the highland form and the two putative parental lowland species, and found strong ecological separation between the highland and lowland forms. Second, mitochondrial and nuclear DNA supports the distinction of the highland form from both putative parental species, with mtDNA data refuting the hypothesis that representatives of either species may represent a matrilineal founder. Morphologically, the highland form is significantly smaller than, and otherwise readily differentiated from, both R. brownorum and R. cf. forreri, as well as all other Rana found in Honduras and adjacent areas. As a result, we formally describe the highland leopard frog as a new species.

http://zoobank.org/urn:lsid:zoobank.org:pub:BE53F587-3618-4433-9651-E495808E5474     

Evolutionary Drivers of Diversification and Distribution of a Southern Temperate Stream Fish Assemblage: Testing the Role of Historical Isolation and Spatial Range Expansion

This study used phylogenetic analyses of mitochondrial cytochrome b sequences to investigate genetic diversity within three broadly co-distributed freshwater fish genera (Galaxias, Pseudobarbus and Sandelia) to shed some light on the processes that promoted lineage diversification and shaped geographical distribution patterns. A total of 205 sequences of Galaxias, 177 sequences of Pseudobarbus and 98 sequences of Sandelia from 146 localities across nine river systems in the south-western Cape Floristic Region (South Africa) were used. The data were analysed using phylogenetic and haplotype network methods and divergence times for the clades retrieved were estimated using *BEAST. Nine extremely divergent (3.5–25.3%) lineages were found within Galaxias. Similarly, deep phylogeographic divergence was evident within Pseudobarbus, with four markedly distinct (3.8–10.0%) phylogroups identified. Sandelia had two deeply divergent (5.5–5.9%) lineages, but seven minor lineages with strong geographical congruence were also identified. The Miocene-Pliocene major sea-level transgression and the resultant isolation of populations in upland refugia appear to have driven widespread allopatric divergence within the three genera. Subsequent coalescence of rivers during the Pleistocene major sea-level regression as well as intermittent drainage connections during wet periods are proposed to have facilitated range expansion of lineages that currently occur across isolated river systems. The high degree of genetic differentiation recovered from the present and previous studies suggest that freshwater fish diversity within the south-western CFR may be vastly underestimated, and taxonomic revisions are required.