The Bassian Isthmus and the major ocean currents of southeast Australia influence the phylogeography and population structure of a southern Australian intertidal barnacle Catomerus polymerus (Darwin)

Southern Australia is currently divided into three marine biogeographical provinces based on faunal distributions and physical parameters. These regions indicate eastern and western distributions, with an overlap occurring in the Bass Strait in Victoria. However, studies indicate that the boundaries of these provinces vary depending on the species being examined, and in particular on the mode of development employed by that species, be they direct developers or planktonic larvae dispersers. Mitochondrial DNA sequence analysis of the surf barnacle Catomerus polymerus in southern Australia revealed an east-west phylogeographical split involving two highly divergent clades (cytochrome oxidase I 3.5 +/- 0.76%, control region 6.7 +/- 0.65%), with almost no geographical overlap. Spatial genetic structure was not detected within either clade, indicative of a relatively long-lived planktonic larval phase. Five microsatellite loci indicated that C. polymerus populations exhibit relatively high levels of genetic divergence, and fall into four subregions: eastern Australia, central Victoria, western Victoria and Tasmania, and South Australia. F(ST) values between eastern Australia (from the eastern mitochondrial DNA clade) and the remaining three subregions ranged from 0.038 to 0.159, with other analyses indicating isolation by distance between the subregions of western mitochondrial origin. We suggest that the east-west division is indicative of allopatric divergence resulting from the emergence of the Bassian land-bridge during glacial maxima, preventing gene flow between these two lineages. Subsequently, contemporary ecological conditions, namely the East Australian, Leeuwin, and Zeehan currents and the geographical disjunctions at the Coorong and Ninety Mile Beach are most likely responsible for the four subregions indicated by the microsatellite data.     

The complete mitochondrial genome of two recently derived species of the fish genus <Emphasis Type="Italic">Nannoperca</Emphasis> (Perciformes,Percichthyidae)

Here we report the complete sequence of mitochondrial genomes for two sister taxa of freshwater teleosts, the recently derived Yarra pigmy perch Nannoperca obscura and the southern pigmy perch Nannoperca australis. These represent the first complete mitochondrial genomes for Percichthyidae (Perciformes), a family mostly distributed in Australia. The de novo genome assembly of 316,430 pyrosequencing reads from 454 libraries has produced the entire mitochondria for N. obscura and a nearly complete version for N. australis. The mtDNA genome from the latter was completed through the design of one primer set and standard Sanger sequencing for genome finishing, followed by the hybrid assembly of reads with MIRA software using N. obscura sequence as reference genome. The complete mitogenomes of N. obscura and N. australis are 16,496 and 16,494 bp in size, respectively. Both genomes contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a control region. Several characteristics of mitochondria typically found in teleost fishes were detected, such as: (i) most genes found in the heavy strand, with the exception of ND6 and eight tRNA genes; (ii) avoidance of G as the third base of codons; (iii) presence of gene overlapping; (iv) percentage of bases usage. We found only eight indels and 197 nucleotide substitutions between these Nannoperca mitogenomes, consistent with a previous hypothesis of recent speciation. The data reported here provide a resource for comparative analysis of recent evolution of mitochondrial genomes.     

Polymorphic microsatellite markers in an Australian freshwater fish,southern pygmy perch Nannoperca australis

Five microsatellite loci were isolated and characterized for the southern pygmy perch, Nannoperca australis, a regionally vulnerable Australian freshwater fish. Screening of 22 individuals from southeastern Australia revealed four to 15 alleles per locus, and observed levels of heterozygosity ranged from 0.09 to 0.45. All loci conformed to Hardy–Weinberg proportions and were in linkage equilibrium.     

Phylogeographic structure in the threatened Yarra pygmy perch <Emphasis Type="Italic">Nannoperca obscura</Emphasis> (Teleostei: Percichthyidae) has major implications for declining populations

Molecular genetic information should be a pre-requisite when evaluating conservation priorities in highly structured species such as freshwater fishes. Nuclear (allozyme) and mitochondrial (cytochrome b) markers were used to investigate phylogeographic structure in the Yarra pygmy perch Nannoperca obscura (Klunzinger), a threatened freshwater fish endemic to mainland south-eastern Australia. Complementary patterns of strong, geographically defined sub-structure were observed including a major east–west divergence (at the Glenelg River), four diagnosable lineages, and statistically-significant differences between most populations. Accordingly, four Evolutionarily Significant Units (ESUs) are defined and multiple, drainage-scale Management Units (MUs) suggested. Since Nannoperca obscura is a relatively poor disperser with no apparent gene flow between most populations, any regional extirpation would see the irreversible loss of genetic diversity. This is problematic, as several populations, most notably a recently discovered ESU in the Murray-Darling Basin, are feared extirpated through a combination of anthropogenic threats and severe drought. The potential loss of unique evolutionarily components within N. obscura soon after their discovery highlights with some urgency, the need to define and protect conservation units in highly modified freshwater habitats.     

Analysis of multilocus DNA reveals hybridization in a contact zone between Empidonax flycatchers

Contact zones between recently diverged taxa offer unique opportunities to test whether the forms are reproductively isolated and therefore distinct species. The Pacific‐slope flycatcher Empidonax difficilis and Cordilleran flycatcher Empidonax occidentalis are closely related taxa that were officially separated into two species in 1989, a treatment that has been controversial due to reports of phenotypically intermediate birds across the southern interior of British Columbia and Alberta. We present the first analysis of molecular variation across this region, in order to determine whether there is genetic introgression between the taxa. Allopatric populations of Pacific‐slope and Cordilleran flycatchers belong to distinct mitochondrial clades, and all of the individuals sampled in interior southwestern Canada have the Pacific‐slope haplotype. In contrast, variation in nuclear DNA (AFLPs) indicates hybridization between Pacific‐slope and Cordilleran flycatchers in this region. We suggest that the discordance between the mitochondrial and nuclear markers most likely results from stochastic loss of Cordilleran mitochondrial haplotype lineages facilitated by asymmetries in mating due to earlier arrival and greater abundance of Pacific‐slope flycatchers in the contact zone. The discovery of hybridization between Pacific‐slope and Cordilleran flycatchers in southwestern Canada may call into question the decision to split them into two species. On the other hand, allopatric populations are genetically distinct in both mitochondrial and nuclear DNA, and the hybridization might not affect populations outside of the contact zone. This study highlights the importance of employing multiple genetic markers in studies of contact zones between closely related species.     

Molecular phylogeny and phylogeography of the Australian freshwater fish genus Galaxiella, with an emphasis on dwarf galaxias (G. pusilla)

The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.     

Patterns of species diversity and endemism in comparable temperate brown algal floras

Brown algal species diversity is compared in 100 km sections of the coastlines of four warm temperate regions: southern Australia, California, southwestern Africa, north-central Chile. The highest diversity (over 140 species per section) is found in southern Australia. California has a reasonable diversity (around 70 species per section), and both southern Australia and California have high regional endemism. Sections of north-central Chile and southwestern Africa have similar patterns, with low diversity (< 30 species per 100 km section), low endemism, few or no fucoids, and up to 25% of the brown algal flora are environmentally tolerant species of Scytosiphonales. Species turnover between contiguous sections of coast is generally related to relative change in temperature regime. Thus the high diversity of southern Australia is due to high species diversity within the 100 km sections, with little turnover, except for a rapid reduction in eastern Victoria likely to be related to lack of rocky substatum. It is hypothesized that low diversity and endemism in Chile and southwestern Africa can be explained by the occurrence of major environmental perturbations (upwelling and El Nino effects) in these regions, producing variable inter-annual temperature conditions that select out tolerant species from the local floras.     

Multilocus phylogeography of Australian teals (Anas spp.): a case study of the relationship between vagility and genetic structure

Biogeographic barriers potentially restrict gene flow but variation in dispersal or vagility can influence the effectiveness of these barriers among different species and produce characteristic patterns of population genetic structure. The objective of this study was to investigate interspecific and intraspecific genetic structure in two closely related species that differ in several life‐history characteristics. The grey teal Anas gracilis is geographically widespread throughout Australia with a distribution that crosses several recognized biogeographic barriers. This species has high vagility as its extensive movements track broad‐scale patterns in rainfall. In contrast, the closely related chestnut teal A. castanea is endemic to the mesic southeastern and southwestern regions of Australia and is more sedentary. We hypothesized that these differences in life‐history characteristics would result in more pronounced population structuring in the chestnut teal. We sequenced five nuclear loci (nuDNA) for 49 grey teal and 23 chestnut teal and compared results to published mitochondrial DNA (mtDNA) sequences. We used analysis of molecular variance to examine population structure, and applied coalescent based approaches to estimate demographic parameters. As predicted, chestnut teal were more strongly structured at both mtDNA and nuDNA (Φ_ST= 0.163 and 0.054, respectively) than were grey teal (Φ_ST < 0.0001 for both sets of loci). Surprisingly, a greater proportion of the total genetic variation was partitioned among populations within species (Φ_SC= 0.014 and 0.047 for nuDNA and mtDNA, respectively) than between the two species (Φ_CT < 0.0001 for both loci). The ‘Isolation with Migration’ coalescent model suggested a late Pleistocene divergence between the taxa, but remarkably, a deeper divergence between the southeastern and southwestern populations of chestnut teal. We conclude that dispersal potential played a prominent role in the structuring of populations within these species and that divergent selection associated with ecology and life history traits likely contributed to rapid and recent speciation in this pair.     

TERTIARY SPECIATION MODELS IN AUSTRALIAN ANURANS: MOLECULAR DATA CHALLENGE PLEISTOCENE SCENARIO

Similarities between frogs in the faunas of southwestern and southeastern Australia have long been viewed as indicators of close genetic relationships and recent (Pleistocene) divergences. We studied albumin evolution in 16 east-west species pairs of frogs representing six genera to assess the validity of these conclusions. Analysis of albumin evolution in western species of Heleioporus and some species of Litoria suggested recent speciation in these genera, with the closest sister groups occurring in the western and not among the eastern fauna. All divergences measured between eastern and western cognate species point to a Tertiary separation extending from the late Miocene to the early Oligocene. Micro-complement fixation studies provide an independent estimation of both genetic relationships between species pairs and the time of divergence of each species pair, allowing the testing of models of speciation and vicariance biogeography in a way not possible with earlier methodologies.     

A molecular phylogeny of New Zealand's Petroica (Aves: Petroicidae) species based on mitochondrial DNA sequences

The New Zealand robin (Petroica australis), tomtit (P. macrocephala), and Chatham Island black robin (P. traversi) are members of the Petroicidae family of Australo-Papuan robins, found throughout Australasia and the western Pacific. In the nearly 200 years since the New Zealand members of Petroicidae were first described, the division of species, subspecies, and even genera has undergone many changes. In this study, we investigate whether molecular phylogenies based on mitochondrial DNA sequences support current taxonomic classifications based on morphology. Petroica traversi, P. australis, and P. macrocephala form distinct clades in phylogenetic trees constructed from Cytochrome b and control region sequences, however the position of the black robin is at odds with the morphological and behavioral data. The black robin does not appear to be a derivative of the New Zealand robin, instead it groups strongly with the tomtit, indicating that lineage sorting and/or introgressive hybridization may have occurred. There is some evidence to support the hypothesis that two invasions of Petroica from Australia have occurred, however additional data from Australian Petroica taxa are required to confirm this. Control region sequences confirm a deep split between the North and South Island P. australis lineages, but suggest a recent radiation of P. macrocephala.     

The puzzling phylogeography of the haplochromine cichlid fish Astatotilapia burtoni

Astatotilapia burtoni is a member of the “modern haplochromines,” the most species‐rich lineage within the family of cichlid fishes. Although the species has been in use as research model in various fields of research since almost seven decades, including developmental biology, neurobiology, genetics and genomics, and behavioral biology, little is known about its spatial distribution and phylogeography. Here, we examine the population structure and phylogeographic history of A. burtoni throughout its entire distribution range in the Lake Tanganyika basin. In addition, we include several A. burtoni laboratory strains to trace back their origin from wild populations. To this end, we reconstruct phylogenetic relationships based on sequences of the mitochondrial DNA (mtDNA) control region (d‐loop) as well as thousands of genomewide single nucleotide polymorphisms (SNPs) derived from restriction‐associated DNA sequencing. Our analyses reveal high population structure and deep divergence among several lineages, however, with discordant nuclear and mtDNA phylogenetic inferences. Whereas the SNP‐based phylogenetic hypothesis uncovers an unexpectedly deep split in A. burtoni, separating the populations in the southern part of the Lake Tanganyika basin from those in the northern part, analyses of the mtDNA control region suggest deep divergence between populations from the southwestern shoreline and populations from the northern and southeastern shorelines of Lake Tanganyika. This phylogeographic pattern and mitochondrial haplotype sharing between populations from the very North and the very South of Lake Tanganyika can only partly be explained by introgression linked to lake‐level fluctuations leading to past contact zones between otherwise isolated populations and large‐scale migration events.     

Molecular phylogeny of hipposiderid bats (Chiroptera: Hipposideridae) from Solomon Islands and Cape York Peninsula,Australia

Throughout the Old World Tropics, examples of cryptic diversity have been demonstrated in leaf‐nosed bats from the Family Hipposideridae. In addition to cryptic diversity, the widespread distributions and graded morphologies of some species render the taxonomy of this family poorly resolved. We used sequences of the mitochondrial gene ND2 and the nuclear gene RAG1 to reconstruct molecular phylogenetic relationships for hipposiderid species. Specimens from Solomon Island and Cape York Peninsula, Australia, were sequenced and combined with published sequences from Southeast Asia. Our results suggest the presence of undescribed diversity in northern Australia. Sequences of ND2 and RAG1 for samples of Cape York Hipposideros ater were distinct from those of Southeast Asia, with corrected sequence divergence estimates for the mitochondrial gene exceeding 23%. In comparison, there was no cryptic diversity detected in Solomon Island specimens when compared to conspecifics from Southeast Asia. On the contrary, three species members of the diadema morphological group from the region exhibit variability in the mitochondrial gene ND2, far below that of other species included in the analyses.     

Sympatric Australian Lasaea species (Mollusca: Bivalvia) differ in their ploidy levels, reproductive modes and developmental modes

The cosmopolitan marine bivalve genus Lasaea is predominantly composed of highly polyploid asexual lineages with one exception: the diploid, sexual Australian species L. australis. Two undescribed, direct-developing congeners co-occur with the indirect-developing L. australis on the rocky intertidal of southeastern Australia. One of these, L. colmani sp. nov., is also diploid and sexual. The other direct-developing congener is an asexual polyploid composed of a variety of clonal lineages. All three sympatric Australian Lasaea congeners are morphologically distinguishable, although prodissoconch distinctions are required to separate large polyploid clams from equivalently-sized L. australis. Similarities in mitochondrial gene sequence and in shell morphology suggest that L. australis and the Australian sympatric polyploid clones share an exclusive common ancestor despite differing in developmental mode, ploidy and reproductive mode. However, detailed karyological analyses failed to identify a chromosome set morphologically similar to that of L. australis among the sympatric Australian polypoid complement. We propose that generation of the polyploid Australian clones (presumably by hybridization) was followed by radical karyological rearrangement.     

Nuptial coloration varies with ambient light environment in a freshwater fish

Visual signals play a vital role in many animal communication systems. Signal design, however, often varies within species, raising evolutionarily important questions concerning the maintenance of phenotypic diversity. We analysed nuptial colour variation within and among nine populations of southern pygmy perch (Nannoperca australis Günther) along an environmental light gradient. Within populations, larger males were redder and blacker, and better-condition males were blacker. Among populations, red colour was positively correlated with the amount of orange-red light present, suggesting that males are likely optimizing signal conspicuousness by producing proportionally larger and redder patches in broad spectrum environments with more orange-red light. Signal contrast, in this regard, is maximized when red colour, appearing bright because of the prevalence of red wavelengths, is viewed against the water-column background. Together, our results are concordant with the sensory drive hypothesis; selection favours signal adaptations or signal plasticity to ensure communication efficacy is maximized in different light environments.     

Historical demography and colonization pathways of the widespread intertidal seaweed Hormosira banksii (Phaeophyceae) in southeastern Australia

The palaeoceanography of southern Australia has been characterized by fluctuating sea levels during glacial periods, changing temperature regimes and modified boundary currents. Previous studies on genetic structuring of species in southeastern Australia have focused mainly on the differentiation of eastern and western populations while the potential role of Bass Strait as a region of overlap for three biogeographic provinces (Peronia, Maugea, and Flindersia) has been largely ignored. This study aimed to explore the likely roles of historic and contemporary factors in determining divergence patterns in the habitat‐forming intertidal seaweed Hormosira banksii in southeastern Australia with a special focus on postglacial dispersal into Bass Strait. We examined the genetic diversity of 475 Hormosira specimens collected from 19 sites around southern Australia using DNA sequence analysis of cytochrome oxidase 1. Three major haplotype groups were identified (western, centre and eastern) corresponding with the three existing biogeographical provinces in this region. Historic break points appeared to be retained and reinforced by modern day dispersal barriers. Phylogeographic grouping of Hormosira reflected a combination of historic and contemporary oceanography. As western and eastern group haplotypes were largely absent within Bass Strait, re‐colonization after the last glacial maximum appeared to have originated from refuges within or near present day Bass Strait. Patterns of genetic structure for Hormosira are consistent with other marine species in this region and highlight the importance of biogeographical barriers in contributing to modern genetic structure.     

Screening mitochondrial DNA sequence variation as an alternative method for tracking established and outbreak populations of Queensland fruit fly at the species southern range limit

Understanding the relationship between incursions of insect pests and established populations is critical to implementing effective control. Studies of genetic variation can provide powerful tools to examine potential invasion pathways and longevity of individual pest outbreaks. The major fruit fly pest in eastern Australia, Queensland fruit fly Bactrocera tryoni (Froggatt), has been subject to significant long‐term quarantine and population reduction control measures in the major horticulture production areas of southeastern Australia, at the species southern range limit. Previous studies have employed microsatellite markers to estimate gene flow between populations across this region. In this study, we used an independent genetic marker, mitochondrial DNA (mtDNA) sequences, to screen genetic variation in established and adjacent outbreak populations in southeastern Australia. During the study period, favorable environmental conditions resulted in multiple outbreaks, which appeared genetically distinctive and relatively geographically localized, implying minimal dispersal between simultaneous outbreaks. Populations in established regions were found to occur over much larger areas. Screening mtDNA (female) lineages proved to be an effective alternative genetic tool to assist in understanding fruit fly population dynamics and provide another possible molecular method that could now be employed for better understanding of the ecology and evolution of this and other pest species.     

Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species group

Palaeoclimatic events and biogeographical processes since the mid-Tertiary are believed to have strongly influenced the evolution and distribution of the terrestrial vertebrate fauna of southeastern Australia. We examined the phylogeography of the temperate-adapted members of the Egernia whitii species group, a group of skinks that comprise both widespread low- to mid-elevation (E. whitii) and montane-restricted species (Egernia guthega, Egernia montana), in order to obtain important insights into the influence of past biogeographical processes on the herpetofauna of southeastern Australia. Sequence data were obtained from all six temperate-adapted species within the E. whitii species group, and specifically from across the distributional ranges of E. whitii, E. guthega and E. montana. We targeted a fragment of the ND4 mitochondrial gene (696 bp) and analysed the data using maximum likelihood and Bayesian methods. Our data reveal a deep phylogeographical break in the east Gippsland region of Victoria between 'northern' (Queensland, New South Wales, Australian Capital Territory) and 'southern' (Victoria, Tasmania, South Australia) populations of E. whitii. This divergence appears to have occurred during the late Miocene-Pliocene, with the Gippsland basin possibly forming a geographical barrier to dispersal. Substantial structuring within both the 'northern' and the 'southern' clades is consistent with the effects of Plio-Pleistocene glacial-interglacial cycles. Pleistocene glacial cycles also appear to have shaped the phylogeographical patterns observed in the alpine species, E. guthega and E. montana. We used our results to examine the biogeographical process that led to the origin and subsequent diversification of the lowland and alpine herpetofauna of southeastern Australia.     

A new dolphin species, the Burrunan Dolphin Tursiops australis sp. nov., endemic to southern Australian coastal waters

Small coastal dolphins endemic to south-eastern Australia have variously been assigned to described species Tursiops truncatus, T. aduncus or T. maugeanus; however the specific affinities of these animals is controversial and have recently been questioned. Historically 'the southern Australian Tursiops' was identified as unique and was formally named Tursiops maugeanus but was later synonymised with T. truncatus. Morphologically, these coastal dolphins share some characters with both aforementioned recognised Tursiops species, but they also possess unique characters not found in either. Recent mtDNA and microsatellite genetic evidence indicates deep evolutionary divergence between this dolphin and the two currently recognised Tursiops species. However, in accordance with the recommendations of the Workshop on Cetacean Systematics, and the Unified Species Concept the use of molecular evidence alone is inadequate for describing new species. Here we describe the macro-morphological, colouration and cranial characters of these animals, assess the available and new genetic data, and conclude that multiple lines of evidence clearly indicate a new species of dolphin. We demonstrate that the syntype material of T. maugeanus comprises two different species, one of which is the historical 'southern form of Tursiops' most similar to T. truncatus, and the other is representative of the new species and requires formal classification. These dolphins are here described as Tursiops australis sp. nov., with the common name of 'Burrunan Dolphin' following Australian aboriginal narrative. The recognition of T. australis sp. nov. is particularly significant given the endemism of this new species to a small geographic region of southern and south-eastern Australia, where only two small resident populations in close proximity to a major urban and agricultural centre are known, giving them a high conservation value and making them susceptible to numerous anthropogenic threats.     

Three divergent lineages within an Australian marsupial (Petrogale penicillata) suggest multiple major refugia for mesic taxa in southeast Australia

Mesic southeastern Australia represents the continent's ancestral biome and is highly biodiverse, yet its phylogeographic history remains poorly understood. Here, we examine mitochondrial DNA (mtDNA) control region and microsatellite diversity in the brush‐tailed rock‐wallaby (Petrogale penicillata; n = 279 from 31 sites), to assess historic evolutionary and biogeographic processes in southeastern Australia. Our results (mtDNA, microsatellites) confirmed three geographically discrete and genetically divergent lineages within brush‐tailed rock‐wallabies, whose divergence appears to date to the mid‐Pleistocene. These three lineages had been hypothesized previously but data were limited. While the Northern and Central lineages were separated by a known biogeographic barrier (Hunter Valley), the boundary between the Central and Southern lineages was not. We propose that during particularly cool glacial cycles, the high peaks of the Great Dividing Range and the narrow adjacent coastal plain resulted in a more significant north–south barrier for mesic taxa in southeastern Australia than has been previously appreciated. Similarly, located phylogeographic breaks in codistributed species highlight the importance of these regions in shaping the distribution of biodiversity in southeastern Australia and suggest the existence of three major refuge areas during the Pleistocene. Substructuring within the northern lineage also suggests the occurrence of multiple local refugia during some glacial cycles. Within the three major lineages, most brush‐tailed rock‐wallaby populations were locally highly structured, indicating limited dispersal by both sexes. The three identified lineages represent evolutionarily significant units and should be managed to maximize the retention of genetic diversity within this threatened species.