Population structure in the freshwater shrimp (Paratya australiensis) inferred from allozymes and mitochondrial DNA

In 1995, an allozyme study was conducted on the genetic structure of a population of the common atyid shrimp, Paratya australiensis, in the Conondale Range, south-eastern Queensland with two subcatchments each within two river drainages sampled. The allozyme study revealed a high degree of population structure, with the data interpreted as reflecting a pattern of restricted contemporary gene flow, primarily between streams within subcatchments. High levels of differentiation occurred between all subcatchments. In this study, we analysed a partial fragment of the mitochondrial COI gene in order to further test and verify these results. The mtDNA data largely conflicted with the hypothesis of restricted gene flow indicating that contemporary dispersal was highly unlikely, even between streams within subcatchments, with many sites fixed for unique mtDNA haplotypes. Additionally, the level of divergence between the Stony Creek subcatchment and all other sampling sites indicated that it had been isolated for approximately 2-3 million years, while low levels of divergence were detected across the Conondale Range between the Kilcoy and Booloumba Creek subcatchments. The sharing of alleles at certain allozyme loci between all subcatchments is, therefore, likely to be the result of ancestral retention and possibly because of the effects of balancing selection.     

Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life history transition in phylogeographic diversification

The widespread distribution of the freshwater shrimp Paratya australiensis in eastern Australia suggests that populations of this species have been connected in the past. Amphidromy is ancestral in these shrimps, although many extant populations are known to be restricted to freshwater habitats. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to examine diversity within P. australiensis and to assess the relative importance of amphidromy in its evolutionary history. We hypothesized that if transitions from an amphidromous to a freshwater life history were important, then we would find a number of divergent lineages restricted to single or groups of nearby drainages. Alternatively, if amphidromy was maintained within the species historically, we expected to find lineages distributed over many drainages. We assumed that the only way for divergence to occur within amphidromous lineages was if dispersal was limited to between nearby estuaries, which, during arid periods in the earth's history, became isolated from one another. We found nine highly divergent mtDNA lineages, estimated to have diverged from one another in the late Miocene/early Pliocene, when the climate was more arid than at present. Despite this, the geographic distribution of lineages and haplotypes within lineages did not support the notion of a stepping-stone model of dispersal between estuaries. We conclude that the extensive divergence has most likely arisen through a number of independent amphidromy-freshwater life history transitions, rather than via historical isolation of amphidromy populations. We also found evidence for extensive movement between coastal and inland drainages, supporting the notion that secondary contact between lineages may have occurred as a result of drainage rearrangements. Finally, our data indicate that P. australiensis is likely a complex of cryptic species, some of which are widely distributed, and others geographically restricted.     

The relationship between egg size and embryonic and larval development in the freshwater shrimp Paratya australiensis Kemp (Decapoda: Atyidae)

1. Paratya australiensis egg and clutch sizes vary between lower and upper altitude sites within headwater streams of the Conondale Range, Queensland, Australia. The adaptive significance of this variation is examined by comparing the development of large eggs from upper sites with small eggs from lower sites at ambient temperatures in the laboratory. 2. Embryonic duration was not dependent on egg size, but was a function of temperature (28 days at 18 °C, but only 22 days at 21 °C). However, larvae developing from large eggs were significantly larger at all stages of development, larval duration was shorter and growth rate was faster than that of larvae from small eggs. 3. It is suggested that the larger, more rapidly developing larvae at upper altitude sites have a greater chance of maintaining position within headwater sections of the stream. This is important as physical barriers such as waterfalls may severely restrict upstream movement. At lower altitude sites, maintaining position may not be as critical as there are no major barriers to upstream movement following downstream displacement. The influence of temperature may also be important as larger eggs may be an adaptation to compensate for slower development of eggs and larvae at cooler, upper altitude sites. The advantage in completing larval development quickly is that larvae would have less risk of removal by spates occurring late in the breeding season.     

Secondary contact followed by gene flow between divergent mitochondrial lineages of a widespread Neotropical songbird (Zonotrichia capensis)

Understanding how genetic and phenotypic differences that arise in geographically isolated populations influence the outcome of secondary contact advances our knowledge of speciation. In the present study, we investigate the secondary contact between divergent lineages of a widespread Neotropical songbird, the Rufous‐collared sparrow (Zonotrichia capensis). Zonotrichia capensis is morphologically and behaviourally diverse, and shows a pattern of lineage diversification produced by a Pleistocene expansion and colonization of South America from a probable Central American origin. Consistent with previous results, we find three lineages throughout the species range, showing between 1.5% and 2.5% divergence in mitochondrial control region sequences. These lineages come into secondary contact in the Dominican Republic, La Paz (Bolivia), and North‐eastern Argentina. We use DNA microsatellite data to study a broad secondary contact zone in North‐eastern Argentina, finding that Bayesian clustering analyses do not assign individuals to their respective mitochondrial lineages. Overall, we did not observe nuclear genetic discontinuities in the study area. We conclude that, if genetic, morphological, and/or cultural differences accumulated among lineages during isolation, they were insufficient to prevent gene flow after secondary contact. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 863–868.     

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.     

Bank voles in linear habitats show restricted gene flow as revealed by mitochondrial DNA (mtDNA)

Genetic structure of bank vole populations in linear river bank habitat in southeast Norway was determined from analyses of DNA sequences for the mitochondrial D-loop. Animals were sampled at sites separated by 1 km, along two forested river banks separated by ≈ 100 m of open water. Twenty-six distinct haplotypes were found among 120 voles. The voles showed significant deviation from panmixis on both sides of the river. Animals from the same site or from sites 1 km apart were more likely to share haplotypes than animals 2 km apart or more. Common haplotypes were widespread on both river banks, and had a wider distribution than relatively rare haplotypes. Some rare haplotypes were found on both banks, but most were restricted to a single bank. The results suggest that short-term gene flow may be restricted for female bank voles in linear habitats. Female territorial behaviour may vary with habitat geometry. In the linear habitat described here, females defend only two territorial borders and may effectively limit female dispersal. Results were compared to a previous study of bank voles from this region in a two-dimensional habitat. Gene flow in the linear habitat was much more restricted than gene flow in the two-dimensional habitat. Probable mechanisms underlying this difference are discussed.     

Hybrid swarm between divergent lineages of mule deer (Odocoileus hemionus)

Studies of hybrid zones have revealed an array of evolutionary outcomes, yet the underlying structure is typically characterized as one of three types: a hybrid zone, a hybrid swarm or a hybrid taxon. Our primary objective was to determine which of these three structures best characterizes a zone of hybridization between two divergent lineages of mule deer (Odocoileus hemionus), mule deer and black-tailed deer. These lineages are morphologically, ecologically and genetically distinct, yet hybridize readily along a zone of secondary contact between the east and west slopes of the Cascade Mountains (Washington and Oregon, USA). Using microsatellite and mitochondrial DNA, we found clear evidence for extensive hybridization and introgression between lineages, with varying degrees of admixture across the zone of contact. The pattern of hybridization in this region closely resembles a hybrid swarm; based on data from 10 microsatellite loci, we detected hybrids that extend well beyond the F1 generation, did not detect linkage disequilibrium at the centre of the zone and found that genotypes were associated randomly within the zone of contact. Introgression was characterized as bidirectional and symmetric, which is surprising given that the zone of contact occurs along a sharp ecotone and that lineages are characterized by large differences in body size (a key component of mating success). Regardless of the underlying mechanisms promoting hybrid swarm maintenance, it is clear that the persistence of a hybrid swarm presents unique challenges for management in this region.     

Revealing unknown or extinct lineages within Isoetes (Isoetaceae) using DNA sequencesfrom hybrids

Iso?tes, a heterosporous lycopod with a fossil record dating back to the Paleozoic, has numerous putative allopolyploids (resulting from hybridization events coupled with doubling of chromosome number). By using the highly variable nucleotide sequences from the second intron of a LFY homologue in Iso?tes, species could be delimited and hybrid origins determined. The data suggest that reticulate evolution is both common and complex within a more derived species complex of Iso?tes. Sequences of identifiable parentage and sequences that are unlike any diploid species known were recovered, leading to the conclusion that one or both of the putative parents have not yet been discovered or are extinct. A range of observations concerning allopolyploid speciation were categorized as follows: (1) verification of previous hypotheses regarding parentage (e.g., I. riparia, I. appalachiana), (2) determination that two morphologically distinct allotetraploid species can share the same parentage (I. azorica and I. acadiensis), (3) recognition of a cryptic allotetraploid species, indicated by the presence of different parental genomes (I. "appalachiana" from Florida), and (4) identification of allotetraploid species with one or two unknown parents (e.g., I. tuckermanii, I. acadiensis, I. azorica, and I. hyemalis). Some sequences from diploid species are remarkably uniform among populations (e.g., I. echinospora from various locations in North America, Iceland, and Wales), while others are variable at the subspecies level (e.g., northern and southern populations within I. engelmannii).     

A comparative analysis of population structuring and genetic diversity in sympatric lineages of freshwater shrimp (Atyidae: Paratya): concerted or independent responses to hydrographic factors?

1. We determined whether two sympatric mitochondrial DNA (mtDNA) lineages of freshwater shrimp (Decapoda: Atyidae: Paratya australiensis) represent biological species and if they had concerted or independent population responses to hydrographic factors in small streams (the Granite Creeks) in southeastern Australia. 2. Allozyme data indicated the presence of two gene pools at sites where the P. australiensis lineages were co‐occurring and the gene pools were statistically assigned with high probability to each respective lineage. This indicated that these mtDNA lineages in P. australiensis were reproductively isolated and thus biological species. 3. Populations of both lineages were genetically homogeneous among lowland sites within streams, but were isolated by steep stream gradients among upland sites and for lowland–upland site comparisons. However, the magnitude of differentiation was markedly different between the two lineages. Allozyme diversity also differed between the two lineages, suggesting that they have different effective population sizes. Thus, differences in the magnitude of genetic divergence among populations were probably because of different life‐history characteristics, including dispersal ability and population size. 4. Genetic population structure was mostly temporally stable, despite the extreme effects of drought during the first year and substantial stream‐flow during the second. However, stable isotope analyses revealed greater local movement in both lineages during the second year, as greater hydrological connectivity provided more opportunities for dispersal. Thus, although lowland populations within streams were genetically homogeneous, stable isotope data indicated that connections may be sporadic and result from accumulated small‐scale movements among refugial pools. 5. Both lineages were therefore found to have similar small‐scale population responses to the unstable habitats of the Granite Creeks. Results highlight the importance of refugia for the capacity of biota to recover from drought and the need for multiple restored patches to reinstate natural population processes (e.g. resilience, recolonization) in degraded systems.     

A transcriptome-wide assessment of differentially expressed genes among two highly divergent,yet sympatric,lineages of the freshwater Atyid shrimp, <Emphasis Type="Italic">Paratya australiensis</Emphasis>

The current study evaluated the possible toxic effects of the water-soluble fraction of crude oil on the general cellular stress-response mechanisms of two dominant representatives of Lake Baikal’s littoral community, the endemic amphipod species Eulimnogammarus verrucosus and E. cyaneus. The acute toxicity effects on the cellular stress-response mechanisms of amphipods were studied in the laboratory by exposing amphipods in water from Lake Baikal to addition of a water-soluble fraction of crude oil at concentrations considered safe for the aquatic environment. The present study found that even short-term exposure to a water-soluble fraction of crude oil at concentration of 50 µg/L, established as the threshold limit for fishery and aquaculture water reservoirs in the Russian Federation, directly affected the general stress-response markers HSP70 and lipid peroxidation and significantly changed the activity of antioxidant enzymes in both studied species. This result confirms the high sensitivity of Baikal endemics to crude oil. Thus, it also indicates that established standards and threshold limit values of oil concentrations estimated for ecological monitoring of general water reservoirs cannot be applied directly to the unique Lake Baikal ecosystem.     

Delimitation of major lineages within Cuscuta subgenus Grammica (Convolvulaceae) using plastid and nuclear DNA sequences

Subgenus Grammica, the largest and most diverse group in the parasitic genus Cuscuta, includes 130 species distributed primarily throughout the New World, with Mexico as its center of diversity. To circumscribe the subgenus and assess the relationships among its major lineages, we conducted the first phylogenetic study of Grammica using plastid trnL-F and nrITS sequences from a wide taxonomic sampling covering its morphological, physiological, and geographical diversity. With the exception of one species belonging elsewhere, the subgenus was found to be monophyletic. The results further indicate the presence of 15 well-supported major clades within Grammica. Some of those lineages correspond partially to earlier taxonomic treatments, but the majority of groups are identified in this study for the first time. The backbone relationships among major clades, however, remain weakly supported or unresolved in some cases. The phylogenetic results indicate that the fruit dehiscence character is homoplastic, thus compromising its value as a major taxonomic and evolutionary feature. While several striking cases of long-distance dispersal are inferred, vicariance emerges as the most dominant biogeographical pattern for Cuscuta. Species placed within one of the clades with a predominantly South American distribution are hypothesized to have substantially altered plastid genomes.     

Patterns of polymorphism and gene flow of gender-associated mitochondrial DNA lineages in European mussel populations

Mussels of the genus Mytilus have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally and the F type is transmitted maternally. RFLP analysis is used to assess phylogenetic relationships and nucleotide diversity and divergence for both mtDNA genomes in European populations of M. edulis and Atlantic and Mediterranean forms of M. galloprovincialis. Ten restriction endonucleases were used to assay variation in regions of the ND2 and COIII genes for a total of 77 individuals. F and M genomes show a concordant phylogenetic split into two major divergent clades, one specific to Mediterranean M. galloprovincialis and the other containing haplotypes from the three taxa. For both genomes, the geographical distribution of mtDNA variation suggests: (i) extensive levels of mtDNA introgression; (ii) asymmetric mtDNA gene flow from Atlantic to Mediterranean populations; and (iii) recurrent historical hybridization events. Significantly higher mtDNA diversity and divergence are observed for the M than F genome in all three Mytilus taxa, although the evolutionary forces responsible for these differences cannot be resolved. The extensive mtDNA gene flow between European Mytilus taxa conflicts with the restricted mtDNA introgression observed in American mussels , implying geographical variation in the nature of nuclear/mtDNA interactions regulating biparental inheritance.     

Asymmetric and differential gene introgression at a contact zone between two highly divergent lineages of field voles (Microtus agrestis)

Secondary contact zones have the potential to shed light on the mode and rate at which reproductive isolation accumulates during allopatric speciation. We investigated the population genetics of a contact zone between two highly divergent lineages of field voles (Microtus agrestis) in the Swiss Jura mountains. To shed light on the processes underlying introgression, we used maternally, paternally, and bi-parentally inherited markers. Though the two lineages maintained a strong genetic structure, we found some hybrids and evidence of gene flow. The extent of introgression varied with the mode of inheritance, being highest for mtDNA and absent for the Y chromosome. In addition, introgression was asymmetric, occurring only from the Northern to the Southern lineage. Both patterns seem parsimoniously explained by neutral processes linked to differences in effective sizes and sex-biased dispersal rates. The lineage with lower effective population size was also the more introgressed, and the mode-of-inheritance effect correlated with the male-biased dispersal rate of microtine rodents. We cannot exclude, however, that Haldane's effect contributed to the latter, as we found a marginally significant deficit in males (the heterogametic sex) among hybrids. We propose a possible demographic scenario to account for the patterns documented, and empirical extensions to further investigate this contact zone.     

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)

Genomewide markers enable us to study genetic differentiation within a species and the factors underlying it at a much higher resolution than before, which advances our understanding of adaptation in organisms. We investigated genomic divergence in Metrosideros polymorpha, a woody species that occupies a wide range of ecological habitats across the Hawaiian Islands and shows remarkable phenotypic variation. Using 1659 single nucleotide polymorphism (SNP) markers annotated with the genome assembly, we examined the population genetic structure and demographic history of nine populations across five elevations and two ages of substrates on Mauna Loa, the island of Hawaii. The nine populations were differentiated into two genetic clusters distributed on the lower and higher elevations and were largely admixed on the middle elevation. Demographic modelling revealed that the two genetic clusters have been maintained in the face of gene flow, and the effective population size of the high‐altitude cluster was much smaller. A F_ST‐based outlier search among the 1659 SNPs revealed that 34 SNPs (2.05%) were likely to be under divergent selection and the allele frequencies of 21 of them were associated with environmental changes along elevations, such as temperature and precipitation. This study shows a genomic mosaic of M. polymorpha, in which contrasting divergence patterns were found. While most genomic polymorphisms were shared among populations, a small fraction of the genome was significantly differentiated between populations in diverse environments and could be responsible for the dramatic adaptation to a wide range of environments.     

Historical transoceanic dispersal of a freshwater shrimp: the colonization of the South Pacific by the genus Paratya (Atyidae)

Aim To infer the phylogenetic relationships within the freshwater shrimp genus Paratya Miers, 1882 (Atyidae) and to use these data to answer biogeographical questions about the location, timing and form of evolution of this genus in the South Pacific. Location Paratya are spread throughout various freshwater habitats in the western Pacific, with a disjunct northern range in the North Pacific (Japan, Korea, Ryukyu Islands, Siberia) and South Pacific (Australia, New Zealand, New Caledonia, Lord Howe, Norfolk Island). Methods Specimens were obtained from throughout its range. Mitochondrial sequences of cytochrome oxidase subunit I and 16S ribosomal DNA were analysed using phylogenetic techniques to identify whether landmasses are monophyletic and what the relationships are between landmasses. Molecular clock dating methods were used to date divergences between taxa. Results Each landmass was recovered as monophyletic. Japan/Ryukyu Islands is the most basal group, followed by New Zealand. Australian specimens form a sister group to a clade made up of two groups (New Caledonia and Lord Howe/Norfolk Island). The oldest divergence within the genus (between North and South Pacific) took place 12–19 Ma. Main conclusions The geographical origin of the genus (either Gondwana or Laurasia) is unclear. Dispersal occurred between the North and South Pacific long after the split up of Gondwana. Dispersal likely explains the presence of Paratya on each landmass in the South Pacific, from continent to isolated oceanic island. This dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya, given that amphyidromy is plesiomorphic in atyid shrimp.     

Geographical distributions of mitochondrial DNA lineages reflect ancient directions of river flow: a case study of the Japanese freshwater shrimp Neocaridina denticulata denticulata (Decapoda: Atyidae)

The mitochondrial DNA phylogeographical structure of the freshwater atyid shrimp Neocaridina denticulata denticulata was investigated near the Yura and Kako Rivers in western Japan. To assess the biological significance of drainage evolution, fragments of 390 base pairs (bp) extending from the NADH dehydrogenase subunit 2 gene to the tryptophan transfer RNA gene were sequenced for 246 specimens from twenty locations. The phylogenetic tree detected two distinct clades corresponding to the region along the Sea of Japan and Seto Inland Sea, respectively. Geographical mapping of the two clades well reflected the river capture, in which the upper reaches of the Yura River draining into the Sea of Japan had been captured from the Kako River into the Seto Inland Sea. The clear pattern of mitochondrial DNA distribution may be accounted for by the ecological characteristics of species that minimize passive downstream drift, local adaptation, and mountain topography.     

Divergence with gene flow within the recent chipmunk radiation (Tamias)

Increasing data have supported the importance of divergence with gene flow (DGF) in the generation of biological diversity. In such cases, lineage divergence occurs on a shorter timescale than does the completion of reproductive isolation. Although it is critical to explore the mechanisms driving divergence and preventing homogenization by hybridization, it is equally important to document cases of DGF in nature. Here we synthesize data that have accumulated over the last dozen or so years on DGF in the chipmunk (Tamias) radiation with new data that quantify very high rates of mitochondrial DNA (mtDNA) introgression among para- and sympatric species in the T. quadrivittatus group in the central and southern Rocky Mountains. These new data (188 cytochrome b sequences) bring the total number of sequences up to 1871; roughly 16% (298) of the chipmunks we have sequenced exhibit introgressed mtDNA. This includes ongoing introgression between subspecies and between both closely related and distantly related taxa. In addition, we have identified several taxa that are apparently fixed for ancient introgressions and in which there is no evidence of ongoing introgression. A recurrent observation is that these introgressions occur between ecologically and morphologically diverged, sometimes non-sister taxa that engage in well-documented niche partitioning. Thus, the chipmunk radiation in western North America represents an excellent mammalian example of speciation in the face of recurrent gene flow among lineages and where biogeography, habitat differentiation and mating systems suggest important roles for both ecological and sexual selection.     

Geological barriers and restricted gene flow in the holarctic skipper Hesperia comma (Hesperiidae)

Patterns of genetic variation within a species may be a consequence of historical factors, such as past fragmentation, as well as current barriers to gene flow. Using sequence data from the mitochondrial cytochrome oxidase subunit II region (COII) and the nuclear gene wingless, we conducted a phylogeographical study of the holarctic skipper Hesperia comma to elucidate patterns of genetic diversity and to infer historical and contemporary processes maintaining genetic variation. One hundred and fifty-one individuals were sampled from throughout North America and Eurasia, focusing on California and adjacent regions in the western United States where morphological diversity is highest compared to the rest of the range. Analyses of sequence data obtained from both genes revealed a well-supported division between the Old and New World. Within western North America, wingless shows little geographical structure, while a hierarchical analysis of genetic diversity of COII sequences indicates three major clades: a western clade in Oregon and Northern California, an eastern clade including the Great Basin, Rocky Mountains and British Columbia, and a third clade in southern California. The Sierra Nevada and the Transverse Ranges appear to be the major barriers to gene flow for H. comma in the western United States. Relatively reduced haplotype diversity in Eurasia compared to North America suggests that populations on the two continents have been affected by different historical processes.