Phylogeography and Ecology of New Zealand Freshwater Amphipoda (Paracalliope, Paraleptamphopus, and Phreatogammarus)

This thesis examines phylogenetic patterns in three New Zealand amphipod taxa in relation to current geographic distributions and historical climatic (e.g. glaciation, marine inundation) and geological (e.g. mountain building) events using DNA sequencing and distributional data. It also examines how recognition behaviour can be used to delineate potential species boundaries and to assess the role of sexual selection. The endemic genus Phreatogammarus has been found in only a limited number of sites and is not very abundant. An analysis of the genetic variation of two species within the genus using allozyme electrophoresis revealed high levels of genetic differentiation among populations but low levels within populations. This suggested that limited dispersal occurred among habitats with one population possibly representing a cryptic species. The endemic freshwater genus Paraleptamphopus is thought to contain a large number of undescribed species with a number of these existing in small waterbodies such as seepages. Examination of the phylogeographic patterns using both mtDNA (CO1) and nuclear DNA (28S) showed that a number of distinct genetic lineages exist, with CO1 revealing 21 haplotypes with genetic distance of over 20%. Using a molecular clock rate of 2.4%, most haplotypes diverged approximately 8-12 million years ago during the Miocene era, possibly as a result of greater land availability increasing habitat diversity or by allopatric speciation. Morphological and genetic differences were not congruent, with morphologically similar taxa appearing among highly genetically distinct lineages, and some morphologically distinct forms appearing within single lineages. The distribution and habitat variables of 419 sites were analysed to determine what was affecting the presence or absence of Paraleptamphopus. The presence of native vegetation in catchments had a positive affect on Paraleptamphopus distribution suggesting that large anthropogenic changes in catchment vegetation could have a negative effect on their abundance. I found smaller waterbodies to be more important than larger ones highlighting the need to study such sites as rare taxa may be ignored. A better understanding is needed on the role of small waterbodies in promoting overall species diversity in catchments. Examination of Paracalliope fluviatilis phylogenetic patterns using the mtDNA gene CO1 showed that a number of separate clades existed suggesting long term isolation and limited dispersal among catchments. Due to the large genetic divergences among some populations there was the possibility that cryptic species might exist. Species recognition experiments were conducted on seven populations to help determine whether cryptic species were present. For the three most genetically divergent crosses there was bias against inter-population pairings, suggesting that there were between two or three separate species. Using a combined field and laboratory approach, size assortative mating was examined in Paracalliope fluviatilis. The field study showed positive size assortative mating and that larger females carried more eggs, suggesting they were more fecund. A series of laboratory experiments examining four existing theories explaining the phenomenon found that none adequately explained positive size assortative mating in P. fluviatilis. I therefore presented two new explanations to explain size assortative mating: a combination of female resistance and size-related variation in a male's capacity to amplex larger females or a form of indirect intra-sexual competition

Conservation status of New Zealand freshwater invertebrates, 2013

The conservation status of 644 freshwater invertebrate taxa, across five Phyla, 28 Orders and 75 Families, was assessed using the New Zealand Threat Classification System (NZTCS) criteria. Forty-six species were ranked Nationally Critical, 11 Nationally Endangered and 16 Nationally Vulnerable. One hundred and seventy-two taxa were listed as Data Deficient. A full list is presented, along with summaries and brief notes on the most important changes. This list replaces all previous NZTCS lists for freshwater invertebrates

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Phylogeography and species discrimination in the Paracalliope fluviatilis species complex (Crustacea: Amphipoda): can morphologically similar heterospecifics identify compatible mates?

We examined the phylogeographic patterns of Paracalliope fluviatilis (Amphipoda) over its entire range and the prevalence of mate discrimination in laboratory mate choice tests using genetically distinct populations. We predicted that mate discrimination would increase as the level of genetic divergence increased between populations. Thirty different haplotypes were found with pairwise sequence divergences in the range 1–23.5% between locations. Individuals were selected from seven genetically distinct populations and males were presented with 'local' (same population) or 'foreign' (genetically divergent) females. Males were more likely to pair with local than foreign females but there was no evidence of a gradual increase in discrimination. Discrimination became most prominent (approximately 5 : 1 local : foreign) when genetic divergences exceeded approximately 20%; matings between divergent individuals also resulted in significantly fewer females producing eggs. We suggest that: (1) this abrupt shift in discrimination occurs because individuals from different, but similarly divergent, clades rely on different recognition cues (e.g. moulting pheromones with disparate chemical signatures) that trigger recognition and subsequent discrimination of incompatible mates; (2) geological history associated with sea level changes and a series of isolation events may be responsible for the patterns of discrimination that we observed; and (3) amphipods may be more genetically variable relative to other invertebrate taxa

Is size assortative mating in Paracalliope fluviatilis (Crustacea: Amphipoda) explained by male–male competition or female choice?

Field and laboratory studies were used to assess: (1) whether size assortative mating occurred in the New Zealand amphipod Paracalliope fluviatilis and (2) hypotheses developed to explain size assortative mating. We found that assortative mating occurred and that larger females carried more eggs, suggesting they may be more valuable as mates. Laboratory experiments were then used to determine whether: (1) male size influenced the size of the female selected (mechanical constraints hypothesis); (2) male size influenced pairing success in the presence of competition (intrasexual selection hypothesis); (3) take-overs of females occurred and whether large males were more successful (intrasexual selection hypothesis); (4) guard duration varied relative to male and female size (guard duration hypothesis); and (5) females had control over pairing success and guard duration (intersexual selection hypothesis). Although there was evidence to suggest the existence of intrasexual competition for mates (i.e. both small and large males preferred large females), there was no evidence of overt competition (i.e. takeovers of paired females). There was also no difference with respect to how long small and large males guarded females, but large females were guarded longer by both male size classes. Females handicapped by having their mobility reduced were guarded for the same duration as control females but males were more likely to pair with handicapped females, suggesting that they were easier to amplex. Given the lack of evidence for direct male–male competition or female choice, we suggest that assortative mating may be the result of: (1) indirect competition (e.g. in situ large males may be better able to access and amplex the largest females) or (2) female resistance to small males in combination with higher costs that small males may incur in securing large females