title: Testing the effectiveness of the mt DNA Cytochrome c oxidase subunit 1 (COI) gene locus for identifying species of Polychaete worm (Polychaeta: Annelida) in New Zealand

authors: Brett, Christy Donna

subjects: mt DNA

abstract: The ability to accurately identify species is fundamental to ecological research and environmental monitoring. Current taxonomic identifications often rely on differentiation of morphologically ambiguous characters, and a process of categorization which is tedious and often leads to misidentifications. This is compounded by the presence of cryptic taxa, which may be prevalent among Polychaete worms (Polychaeta: Annelida). With increased access to genetic techniques, Cytochrome c oxidase subunit I has been suggested as a possible aid to assist in the discrimination of species resources.
In this study, I tested the hypothesis that the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms.
A 543 base-pair fragment of the COI locus was successfully extracted for 111 individuals from 16 out of 20 morphologically recognised species. Average intraspecific divergences were 0.8 %, ranging from 0 % to 5 %. Average interspecific variation was 26.4 %, ranging from 13.8 % to 36.8 %. The lowest divergences were found between two Nereid species (13.8 %), and two Glycera americana species (17.2 %). Relatively high maximum divergences of over 30 % suggest that some species may have reached a divergence saturation level, which may partially explain why familial groupings in constructed trees were not monophyletic. Divergences within the different Nereid species - a group previously known to have morphologically cryptic species - did not reveal the presence of any cryptic taxa. Pairwise comparisons showed a clear divide between percentages of intra- and interspecific divergences, and the suggested threshold of 11 % is effective for the taxa investigated here.
On the basis of these results, I conclude that sequence variation in the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms, but may not be appropriate for deeper (e.g. generic or familial) phylogenetic relationships among taxa.

text: Testing the effectiveness of the mt DNA Cytochrome c oxidase subunit 1 (COI) gene locus for identifying species of Polychaete worm (Polychaeta: Annelida) in New Zealand The ability to accurately identify species is fundamental to ecological research and environmental monitoring. Current taxonomic identifications often rely on differentiation of morphologically ambiguous characters, and a process of categorization which is tedious and often leads to misidentifications. This is compounded by the presence of cryptic taxa, which may be prevalent among Polychaete worms (Polychaeta: Annelida). With increased access to genetic techniques, Cytochrome c oxidase subunit I has been suggested as a possible aid to assist in the discrimination of species resources.
In this study, I tested the hypothesis that the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms.
A 543 base-pair fragment of the COI locus was successfully extracted for 111 individuals from 16 out of 20 morphologically recognised species. Average intraspecific divergences were 0.8 %, ranging from 0 % to 5 %. Average interspecific variation was 26.4 %, ranging from 13.8 % to 36.8 %. The lowest divergences were found between two Nereid species (13.8 %), and two Glycera americana species (17.2 %). Relatively high maximum divergences of over 30 % suggest that some species may have reached a divergence saturation level, which may partially explain why familial groupings in constructed trees were not monophyletic. Divergences within the different Nereid species - a group previously known to have morphologically cryptic species - did not reveal the presence of any cryptic taxa. Pairwise comparisons showed a clear divide between percentages of intra- and interspecific divergences, and the suggested threshold of 11 % is effective for the taxa investigated here.
On the basis of these results, I conclude that sequence variation in the mtDNA COI gene locus is effective in discriminating morphologically recognised species of Polychaete worms, but may not be appropriate for deeper (e.g. generic or familial) phylogenetic relationships among taxa.

year: 2006

title: The status of fish in Hamilton Lake (Lake Rotoroa)

authors: Kane, Daryl Steven

abstract: The size, population structure, relative fish abundance, diet and heavy metal concentrations of fish in Hamilton Lake (Lake Rotoroa) were examined. A combination of gill nets, fyke nets and minnow traps were used at each of 11 sampling sites located primarily at stormwater inflows around the lake. Sampling was undertaken between 9 December 1993 and 2 March 1994, with one overnight sampling occurring at each site.
A total of 1073 fish were captured, comprising nine different species: catfish (Ictalurus nebulosus), common bully (Gobiomorphus cotidianus), goldfish (Carassius auratus), longfinned eel (Anguilla dieffenbachii), perch (Perca fluviatilis), mosquitofish (Gambusia affinis), rudd (Scardinius erythropthalmus), shortfinned eel (Anguilla australis), and tench (Tinca tinca).
Abundance of rudd has declined since 1990, with a decline in catch rates of 67%. Conversely, perch abundance has increased since 1990, with catch rates increasing by 300%. During this period perch have surpassed rudd as the most abundant fish species. The declines in rudd abundance are probably associated with the disappearance of submerged aquatic macrophytes, largely Egeria densa, from Hamilton Lake during 1990.
Ages of rudd were determined using scales, while perch were aged using opercular bones. Back-calculation of fish length involved the use of both scale proportional (SPH), and body proportional hypotheses (BPH). Results from the SPH appeared more accurate, due to better compatibility with actual observed fish lengths. Sizes of one and two year old rudd appear to have declined over the past six years in Hamilton Lake. In 1987, the mean lengths of one and two year old rudd were 87 mm and 207 mm respectively, while in 1991 the same aged fish were 69 mm and 127 mm in length. Perch growth rates, however, do not appear to have changed. Poorly formed growth rings on both scales and operculum prevented tench from being aged.
Despite the total collapse of submerged aquatic macrophytes, which formed the bulk of the rudd diet (84% by volume), aquatic vegetation still remained the most important food item of adult rudd in the present study, although this now comprised entirely of emergent marginal vegetation. This suggests that rudd >200 mm in length are obligate herbivores. Perch fed largely on invertebrates, before a transition to a largely piscivorous diet at approximately 200 mm in length. Tench appeared to be specialist feeders on molluscs.
Concentrations of four heavy metals (arsenic, lead, copper, and zinc) in the white muscle of fish were examined. Concentrations of the majority of heavy metals analysed were well below maximum permitted levels. Arsenic concentrations were highest in bottom feeding fish, particularly catfish (mean=0.778 mg kg⁻¹ wet weight, compared to the maximum permitted level of 2 mg kg⁻¹ wet weight) due to high arsenic concentrations in the lake sediment resulting from sodium arsenate application for weed control in 1959. Arsenic in the present study was analysed using a dry ashing technique. Arsenic concentrations were higher than those of previous studies in the lake undertaken using a wet ashing technique, which fails to liberate all arsenic from the fish flesh.

text: The status of fish in Hamilton Lake (Lake Rotoroa) The size, population structure, relative fish abundance, diet and heavy metal concentrations of fish in Hamilton Lake (Lake Rotoroa) were examined. A combination of gill nets, fyke nets and minnow traps were used at each of 11 sampling sites located primarily at stormwater inflows around the lake. Sampling was undertaken between 9 December 1993 and 2 March 1994, with one overnight sampling occurring at each site.
A total of 1073 fish were captured, comprising nine different species: catfish (Ictalurus nebulosus), common bully (Gobiomorphus cotidianus), goldfish (Carassius auratus), longfinned eel (Anguilla dieffenbachii), perch (Perca fluviatilis), mosquitofish (Gambusia affinis), rudd (Scardinius erythropthalmus), shortfinned eel (Anguilla australis), and tench (Tinca tinca).
Abundance of rudd has declined since 1990, with a decline in catch rates of 67%. Conversely, perch abundance has increased since 1990, with catch rates increasing by 300%. During this period perch have surpassed rudd as the most abundant fish species. The declines in rudd abundance are probably associated with the disappearance of submerged aquatic macrophytes, largely Egeria densa, from Hamilton Lake during 1990.
Ages of rudd were determined using scales, while perch were aged using opercular bones. Back-calculation of fish length involved the use of both scale proportional (SPH), and body proportional hypotheses (BPH). Results from the SPH appeared more accurate, due to better compatibility with actual observed fish lengths. Sizes of one and two year old rudd appear to have declined over the past six years in Hamilton Lake. In 1987, the mean lengths of one and two year old rudd were 87 mm and 207 mm respectively, while in 1991 the same aged fish were 69 mm and 127 mm in length. Perch growth rates, however, do not appear to have changed. Poorly formed growth rings on both scales and operculum prevented tench from being aged.
Despite the total collapse of submerged aquatic macrophytes, which formed the bulk of the rudd diet (84% by volume), aquatic vegetation still remained the most important food item of adult rudd in the present study, although this now comprised entirely of emergent marginal vegetation. This suggests that rudd >200 mm in length are obligate herbivores. Perch fed largely on invertebrates, before a transition to a largely piscivorous diet at approximately 200 mm in length. Tench appeared to be specialist feeders on molluscs.
Concentrations of four heavy metals (arsenic, lead, copper, and zinc) in the white muscle of fish were examined. Concentrations of the majority of heavy metals analysed were well below maximum permitted levels. Arsenic concentrations were highest in bottom feeding fish, particularly catfish (mean=0.778 mg kg⁻¹ wet weight, compared to the maximum permitted level of 2 mg kg⁻¹ wet weight) due to high arsenic concentrations in the lake sediment resulting from sodium arsenate application for weed control in 1959. Arsenic in the present study was analysed using a dry ashing technique. Arsenic concentrations were higher than those of previous studies in the lake undertaken using a wet ashing technique, which fails to liberate all arsenic from the fish flesh.

year: 1995

title: Traditional Knowledge (TK) Labels Transforming Data Infrastructure to Recognise Indigenous Provenance

authors: Hudson, Maui

subjects: Data

abstract: Associate Professor Maui Hudson, KatieLee Riddle and Dr Janette Hamilton-Pearce introduced the latest developments and applications of the Traditional Knowledge Labels and the Local Contexts Hub with examples of use by researchers in Aotearoa New Zealand.

text: Traditional Knowledge (TK) Labels Transforming Data Infrastructure to Recognise Indigenous Provenance Associate Professor Maui Hudson, KatieLee Riddle and Dr Janette Hamilton-Pearce introduced the latest developments and applications of the Traditional Knowledge Labels and the Local Contexts Hub with examples of use by researchers in Aotearoa New Zealand.

year: 2022-09-27