Jon Waters

Genetic ages for Quaternary topographic evolution: A new dating tool

All eukaryote populations accumulate mutations in their mitochondrial DNA (mtDNA) over time, so reproductively isolated populations become characterized by distinct mtDNA lineages. In addition, the degree of genetic differentiation among distinct populations can be used to estimate time elapsed since their isolation. We have identified an informative system for calibrating the mtDNA “clock” by genetically comparing freshwater galaxiid fish populations isolated in different river drainages. Calibration using a range of Quaternary geological events in southern New Zealand shows that the mtDNA divergence rate in galaxiid fishes is between 1% and 2%/100 k.y. up to 250 k.y., with the rate decreasing with increasing age. The estimated divergence rate slows to around 4%/m.y. for the middle Quaternary, although calibration is poor. A calibration curve has been fitted to all data: divergence (%) = −2.2 e −9 t + 2.5 t + 2.2, where t is isolation age (in m.y.). This molecular clock has potential as a dating tool for glacially related and active tectonic events that have caused river drainage changes in the late Quaternary in the Southern Hemisphere, where galaxiids are widespread. An application of this dating tool to an example in northern South Island uses three different species of freshwater-limited fish, and all three data sets imply formation of a drainage divide at 320 ± 110 ka, at about the time of a major glacial advance though the divide (oxygen isotope stage 8).

Geological and biological evidence for drainage reorientation during uplift of alluvial basins, central Otago, New Zealand

Abstract Three contiguous sedimentary basins at the foot of the Hawkdun Range, central Otago, show evidence for Pleistocene river capture events. The basins formed near the intersection of NNW‐trending and northeast‐trending active structures, along the NNW‐striking Hawkdun Fault zone. The basins are synclinal and have developed between northeast‐trending antiformal ridges. Continuing uplift of two adjacent basins in the late Pleistocene has caused lowering of stream gradients, which encouraged diversion of one river in each basin to the northwest, to lower altitude in the adjacent basin. These reoriented rivers have now cut gorges through growing antiformal ridges, and new low‐relief drainage divides have formed in the basins. These river capture events are notable because they involve basin uplift, not mountain range uplift. We suggest that diversion of one of these rivers, the Ida Burn, into the adjacent basin facilitated interchange of galaxiid fish across the Taieri‐Clutha catchment divide. Spontaneous mutations of mitochondrial DNA (mtDNA) have accumulated in populations of G. anomalus that are now separated by a new drainage divide to the east of the Ida Burn. There has been 1.1 % divergence of mtDNA in fish on either side of this new divide, and an empirical calibration of divergence rates implies that the divide developed c. 60 thousand years (kyr) ago. In contrast, flathead galaxiid species (G. depressiceps and relatives) exhibit 3.5% mtDNA divergence between the Clutha and Taieri catchments, implying separation of these species for c. 500 kyr. Growth and impingement of mountain ranges of the Rough Ridge antiformal complex during the middle Pleistocene may have contributed to isolation of these flathead galaxiid species. Populations of the fish species Galaxias paucispondylus occur in the Hawkdun Basin (Clutha catchment), to the northwest of the other two basins, but not elsewhere in central Otago. A drainage link may have existed between the Hawkdun Basin and the Waitaki valley to the north, where G. paucispondylus is widespread. There is c. 4.2% divergence in mtDNA of G. paucispondylus between these catchments, and an empirical calibration of divergence rates implies that isolation occurred c. 800 kyr ago.

Drainage reorientation in Marlborough Sounds, New Zealand, during the Last Interglacial

Abstract Regional drainage of the Marlborough Sounds area, northern South Island, New Zealand, discharged water and sediment towards the south until the Last Interglacial. Drainage reversal occurred at that time, and discharge is now northwards. Drainage reversal was facilitated by regional subsidence and tilting, and build‐up of a thick (c. 60 m) sedimentary pile in the former main southward axial drainage channel comprising the Kaituna and Are Are valleys (the Kaituna corridor), before the Last Interglacial. Minor southward flow persisted in the Kaituna valley after the Last Interglacial, but this involved locally derived sediments only. Dating of these latter sediments by OSL techniques constrains the minimum age of drainage reversal to be c. 70 ka. The maximum inferred age of reversal (c. 130 ka) is based on regional correlation of glacial outwash terraces. These age estimates are consistent with each other and with geomor‐phological and stratigraphic observations within the Kaituna corridor. The drainage reversal occurred when ponding of sediment in the south allowed overtopping of a low drainage divide farther north in what is now Pelorus Sound. Subsequent erosion through this divide was probably facilitated by shoreline retreat and associated downcutting during sea level high‐stands of the Last Interglacial.

Biological memory of the first Pleistocene glaciation in New Zealand

Living species retain memories of their evolutionary history in their DNA, and that evolutionary history commonly reflects distinct geological events, such as mountain building and glaciation. We synthesize previously documented genetic data for freshwater fishes and a wide range of upland insect and bird species to document the Pliocene and early Pleistocene topographic and glacial history of the Southern Alps of New Zealand. Genetic data for fish suggest that a long, linear mountain chain was established in the Pliocene. At that time, the mountain chain had a tectonically constructed narrow topographic neck in the middle, with wider uplift zones at either end. Separation of populations of upland insects and birds into faunal zones at the wider ends was caused by a major glacial advance at the narrow tectonic neck at 2 ± 0.5 Ma. The composite biological memory constrains the relative timing of uplift of the Southern Alps as a linear mountain chain, with subsequent imposition of temperate glaciation during Pliocene-Pleistocene cooling in the Southern Hemisphere.

Evolution of the Taieri River catchment, East Otago, New Zealand

ABSTRACT This paper synthesises geological and biological data to develop an evolutionary history for the Taieri River that currently follows a circuitous 200 km course as one of the main drainages in Otago. The ancestral Taieri River drained only coastal hills initiated in the Miocene, and much of what is now the upper Taieri catchment flowed into the ancestral Clutha River. Major river reorientation events occurred in the upper half of the catchment because of rise of antiformal fold mountains in the Pleistocene, forming a new divide between the Taieri and Clutha catchments. Coeval incision of a gorge through a volcanic rock barrier connected the upper catchment to the lower Taieri River. The sparse Pleistocene sedimentary record documents these drainage changes via contrasting distribution of distinctive clasts derived from greywacke mountains on the northern edge of the Otago Schist belt. These major capture events are also supported by distributions and genetic divergences of freshwater galaxiid fish species. Erosion during Pleistocene rise of the antiformal mountains caused recycling of placer gold into Clutha tributaries before the Taieri River evolved to its present geometry, thereby limiting the placer gold content of the modern Taieri catchment.

The genealogical sorting index and species delimitation

The Genealogical Sorting Index (gsi) has been widely used in species-delimitation studies, where it is usually interpreted as a measure of the degree to which each of several predefined groups of specimens display a pattern of divergent evolution in a phylogenetic tree. Here we show that the gsi value obtained for a given group is highly dependent on the structure of the tree outside of the group of interest. By calculating the gsi from simulated datasets we demonstrate this dependence undermines some of desirable properties of the statistic. We also review the use of the gsi delimitation studies, and show that the gsi has typically been used under scenarios in which it is expected to produce large and statistically significant results for samples that are not divergent from all other populations and thus should not be considered species. Our proposed solution to this problem performs better than the gsi in under these conditions. Nevertheless, we show that our modified approach can produce positive results for populations that are connected by substantial levels of gene flow, and are thus unlikely to represent distinct species. We stress that the properties of gsi made clear in this manuscript must be taken into account if the statistic is used in species-delimitation studies. More generally, we argue that the results of genetic species-delimitation methods need to be interpreted in the light the biological and ecological setting of a study, and not treated as the final test applied to hypotheses generated by other data.

Genotyping-by-sequencing supports a genetic basis for alpine wing-reduction in a New Zealand stonefly

Wing polymorphism is a prominent feature of numerous insect groups, but the genomic basis for this diversity remains poorly understood. Wing reduction is a commonly observed trait in many species of stoneflies, particularly in cold or alpine environments. The widespread New Zealand stonefly Zelandoperla fenestrata species group (Z. fenestrata, Z. tillyardi, Z. pennulata) contains populations ranging from long-winged (macropterous) to vestigial-winged (micropterous), with the latter phenotype typically associated with high altitudes. The presence of flightless forms on numerous mountain ranges, separated by lowland fully winged populations, suggests wing reduction has occurred multiple times. We use Genotyping by Sequencing (GBS) to test for genetic differentiation between fully winged (n=62) and vestigial-winged (n=34) individuals, sampled from a sympatric population of distinct wing morphotypes, to test for a genetic basis for wing morphology. We found no population genetic differentiation between these two morphotypes across 6,843 SNP loci, however we did detect several outlier loci that strongly differentiated morphotypes across independent tests. This indicates small regions of the genome are likely to be highly differentiated between morphotypes, indicating a genetic basis for morphotype differentiation. These results provide a clear basis for ongoing genomic analysis to elucidate critical regulatory pathways for wing development in Pterygota.