title: Evolution of the genera Vitex (Lamiaceae) and Zygogynum (Winteraceae) on New Caledonia

authors: Pratt, Steven John

abstract: The New Caledonia archipelago is home to a richly diverse flora including a disproportionate number of lineages whose heritage can be traced to ancient Gondwana. Much of this species richness is owed to the complex geologic history, including an extensive period of submersion, of the region which actively shaped the flora over millennia. Given such complexity there is always unknowns both with regards to the circumscription of such a diverse flora and to understanding aspects of the archipelagos geologic past, which in many cases prove extremely difficult to resolve. This thesis investigates two aspects of this notion using modern day molecular techniques. 
The first aspect that we investigate is the question of species circumscription with regards to Vitex (Lamiaceae). Here we scrutinize the monophyly of the morphologically variable species Vitex collina, as described by Mabberley (1990), previously suggested by Mabberley to comprise a minimum of three distinct morphotypes. Additionally we consider the genetic uniqueness of a recently discovered species, tentatively named Vitex sp. “unifolia”, from currently accepted New Caledonian Vitex collina s.l. Maximum likelihood (ML) analyses using the internal transcribed spacer (ITS) genetic loci revealed that New Caledonian Vitex collina is paraphyletic with New Zealand V. lucens and Australian V. lignum-vitae nested within a well-supported V. collina s.l. clade. Our results suggest a minimum of two genetically distinct entities within V. collina, though the new species Vitex sp. “unifolia” was not distinguished genetically from Vitex cf. “collina”. The additional morphological analysis in light of our molecular analyses revealed further distinction of taxa within our sample group. This revealed a potential for three separate morphological entities within Vitex collina s.l. specimens, with Vitex sp. “unifolia” representing a fourth. Further research will result in the formal recognition of Vitex sp. “unifolia” upon publication, as well as further delimitation of the distinct entities within V. collina s.l. These revisions will have implications for the conservation status of these revised species, especially with regards to the rare Vitex sp. “unifolia”.
The second aspect investigated New Caledonian Winteraceae focussing on two research aims. The first aim scrutinised the New Caledonian Zygogynum s.l. in light of revisions made in Vink (1988; 1993; 2003), where four previously recognised genera (Belliolum, Bubbia, Exospermum, and Zygogynum) were dismantled into a single broadly circumscribed genus. The second aim was to assess any major morphological trends within Zygogynum s.l. and biogeographic patterns within the Winteraceae. Maximum Likelihood and Bayesian analyses using the internal transcribed spacer (ITS) and psbA-trnH genetic loci confirmed the monophyly and position of Takhtajania, Tasmannia, Drimys, and Pseudowintera within the Winteraceae. New Caledonian Zygogynum s.l. was shown to be paraphyletic with Z. schlechteri nested within a distinct Australian Bubbia clade separate from remaining Zygogynum. Our analyses showed no support for the distinction of species previously belonging to Belliolum and Exospermum with all remaining Zygogynum forming a monophyletic clade.  The monophyly of species within the Zygogynum were for the most part resolved, with only few species left unresolved or paraphyletic relationships. Further investigation of biogeography within the Winteraceae revealed that Zealandic Winteraceae share their common ancestor with South American taxa, reflecting the Gondwanic roots of this family, with Australian Bubbia having originated from New Caledonian Zygogynum. From this we suggest, upon further investigation, that the retention of Bubbia within Zygogynum s.l. was supported and should be maintained. Alternately, if Bubbia is maintained as distinct from Zygogynum s.l., Z. schlechteri will be revised to Bubbia schlechteri. Further research including specimens of all described taxa will improve the resolution of our analyses, likely identifying further inconsistences that require revision or attention. Our investigation into morphological trends within the Zygogynum uncovered a trend of carpel evolution, in which a single well supported clade of Zygogynum exhibit fused carpels with all others within the family exhibiting unfused gynoecia. The significance of this is that it is a derived trait recognised as a reoccurring trend within the Angiosperm lineage, though this is the first instance where it has been identified occurring within a single genus.

text: Evolution of the genera Vitex (Lamiaceae) and Zygogynum (Winteraceae) on New Caledonia The New Caledonia archipelago is home to a richly diverse flora including a disproportionate number of lineages whose heritage can be traced to ancient Gondwana. Much of this species richness is owed to the complex geologic history, including an extensive period of submersion, of the region which actively shaped the flora over millennia. Given such complexity there is always unknowns both with regards to the circumscription of such a diverse flora and to understanding aspects of the archipelagos geologic past, which in many cases prove extremely difficult to resolve. This thesis investigates two aspects of this notion using modern day molecular techniques. 
The first aspect that we investigate is the question of species circumscription with regards to Vitex (Lamiaceae). Here we scrutinize the monophyly of the morphologically variable species Vitex collina, as described by Mabberley (1990), previously suggested by Mabberley to comprise a minimum of three distinct morphotypes. Additionally we consider the genetic uniqueness of a recently discovered species, tentatively named Vitex sp. “unifolia”, from currently accepted New Caledonian Vitex collina s.l. Maximum likelihood (ML) analyses using the internal transcribed spacer (ITS) genetic loci revealed that New Caledonian Vitex collina is paraphyletic with New Zealand V. lucens and Australian V. lignum-vitae nested within a well-supported V. collina s.l. clade. Our results suggest a minimum of two genetically distinct entities within V. collina, though the new species Vitex sp. “unifolia” was not distinguished genetically from Vitex cf. “collina”. The additional morphological analysis in light of our molecular analyses revealed further distinction of taxa within our sample group. This revealed a potential for three separate morphological entities within Vitex collina s.l. specimens, with Vitex sp. “unifolia” representing a fourth. Further research will result in the formal recognition of Vitex sp. “unifolia” upon publication, as well as further delimitation of the distinct entities within V. collina s.l. These revisions will have implications for the conservation status of these revised species, especially with regards to the rare Vitex sp. “unifolia”.
The second aspect investigated New Caledonian Winteraceae focussing on two research aims. The first aim scrutinised the New Caledonian Zygogynum s.l. in light of revisions made in Vink (1988; 1993; 2003), where four previously recognised genera (Belliolum, Bubbia, Exospermum, and Zygogynum) were dismantled into a single broadly circumscribed genus. The second aim was to assess any major morphological trends within Zygogynum s.l. and biogeographic patterns within the Winteraceae. Maximum Likelihood and Bayesian analyses using the internal transcribed spacer (ITS) and psbA-trnH genetic loci confirmed the monophyly and position of Takhtajania, Tasmannia, Drimys, and Pseudowintera within the Winteraceae. New Caledonian Zygogynum s.l. was shown to be paraphyletic with Z. schlechteri nested within a distinct Australian Bubbia clade separate from remaining Zygogynum. Our analyses showed no support for the distinction of species previously belonging to Belliolum and Exospermum with all remaining Zygogynum forming a monophyletic clade.  The monophyly of species within the Zygogynum were for the most part resolved, with only few species left unresolved or paraphyletic relationships. Further investigation of biogeography within the Winteraceae revealed that Zealandic Winteraceae share their common ancestor with South American taxa, reflecting the Gondwanic roots of this family, with Australian Bubbia having originated from New Caledonian Zygogynum. From this we suggest, upon further investigation, that the retention of Bubbia within Zygogynum s.l. was supported and should be maintained. Alternately, if Bubbia is maintained as distinct from Zygogynum s.l., Z. schlechteri will be revised to Bubbia schlechteri. Further research including specimens of all described taxa will improve the resolution of our analyses, likely identifying further inconsistences that require revision or attention. Our investigation into morphological trends within the Zygogynum uncovered a trend of carpel evolution, in which a single well supported clade of Zygogynum exhibit fused carpels with all others within the family exhibiting unfused gynoecia. The significance of this is that it is a derived trait recognised as a reoccurring trend within the Angiosperm lineage, though this is the first instance where it has been identified occurring within a single genus.

year: 2013

title: An entropy gain measure of numeric prediction performance

authors: Trigg, Leonard E.

subjects: computer science

abstract: Categorical classifier performance is typically evaluated with respect to error rate, expressed as a percentage of test instances that were not correctly classified. When a classifier produces multiple classifications for a test instance, the prediction is counted as incorrect (even if the correct class was one of the predictions). Although commonly used in the literature, error rate is a coarse measure of classifier performance, as it is based only on a single prediction offered for a test instance. Since many classifiers can produce a class distribution as a prediction, we should use this to provide a better measure of how much information the classifier is extracting from the domain. 
Numeric classifiers are a relatively new development in machine learning, and as such there is no single performance measure that has become standard. Typically these machine learning schemes predict a single real number for each test instance, and the error between the predicted and actual value is used to calculate a myriad of performance measures such as correlation coefficient, root mean squared error, mean absolute error, relative absolute error, and root relative squared error. With so many performance measures it is difficult to establish an overall performance evaluation.
The next section describes a performance measure for machine learning schemes that attempts to overcome the problems with current measures. In addition, the same evaluation measure is used for categorical and numeric classifier.

text: An entropy gain measure of numeric prediction performance Categorical classifier performance is typically evaluated with respect to error rate, expressed as a percentage of test instances that were not correctly classified. When a classifier produces multiple classifications for a test instance, the prediction is counted as incorrect (even if the correct class was one of the predictions). Although commonly used in the literature, error rate is a coarse measure of classifier performance, as it is based only on a single prediction offered for a test instance. Since many classifiers can produce a class distribution as a prediction, we should use this to provide a better measure of how much information the classifier is extracting from the domain. 
Numeric classifiers are a relatively new development in machine learning, and as such there is no single performance measure that has become standard. Typically these machine learning schemes predict a single real number for each test instance, and the error between the predicted and actual value is used to calculate a myriad of performance measures such as correlation coefficient, root mean squared error, mean absolute error, relative absolute error, and root relative squared error. With so many performance measures it is difficult to establish an overall performance evaluation.
The next section describes a performance measure for machine learning schemes that attempts to overcome the problems with current measures. In addition, the same evaluation measure is used for categorical and numeric classifier.

year: 1998-05

title: The Daldy Mcwilliams ‘Outrage’ of 1879

authors: Hart, Philip

abstract: In the later 1870s, conflicts developed near Paeroa between a small hapu, Ngati Hako, and other hapu over land sales and surveys. In 1879, after some members of Ngati Koi offered to sell the Pukehanga Block, at Rotokohu, between Paeroa and Te Aroha, to the Crown, surveyors were sent to determine the boundaries despite threats of violence from Ngati Hako. These threats became a reality with shots being fired, wounding a surveyor’s assistant, ‘Daldy’ McWilliams, who survived by playing dead. Despite Pakeha fury about a ‘weak’ response, officials reacted cautiously, fearing to provoke a wider conflict. 
Instead of trying to arrest the two men accused of the attempted murder, which would have been difficult, because Ngati Hako claimed their action was justified the Native Minister encouraged senior Hauraki rangatira to convene a rununga to examine their claim. Ngati Hako said that the block of land was theirs, and as previously other land had been surveyed without their permission they had taken this action. The government was criticized for paying advances on a block that had not been through the land court, and the rununga determined that although Ngati Hako had acted wrongfully, their action could be justified. When Ngati Hako refused to hand over the two accused to the authorities, the rununga claimed not to have the power to hand them over; Ngati Hako then constructed two pa to defend themselves.
Such actions provoked much frustration and criticisms of the government amongst Pakeha, but officials who investigated Ngati Hako’s complaints agreed that they had indeed lost land unjustly. Once the owners of a large domain, they had lost their land to the invading Marutuahu, whose slaves they became. When the two accused were arrested in 1882 one was found not guilty and the other was amnestied after eight months in prison because it was believed that, as rangatira, they probably had not fired the shots but had taken the responsibility for the actions of their hapu. As for McWilliams, he received what he considered inadequate compensation.
This ‘outrage’ was the first and only time in Hauraki that a Maori had shot a Pakeha, and the government’s cautious but firm response meant that the ‘peace of Hauraki’, although disturbed for a while, was maintained.

text: The Daldy Mcwilliams ‘Outrage’ of 1879 In the later 1870s, conflicts developed near Paeroa between a small hapu, Ngati Hako, and other hapu over land sales and surveys. In 1879, after some members of Ngati Koi offered to sell the Pukehanga Block, at Rotokohu, between Paeroa and Te Aroha, to the Crown, surveyors were sent to determine the boundaries despite threats of violence from Ngati Hako. These threats became a reality with shots being fired, wounding a surveyor’s assistant, ‘Daldy’ McWilliams, who survived by playing dead. Despite Pakeha fury about a ‘weak’ response, officials reacted cautiously, fearing to provoke a wider conflict. 
Instead of trying to arrest the two men accused of the attempted murder, which would have been difficult, because Ngati Hako claimed their action was justified the Native Minister encouraged senior Hauraki rangatira to convene a rununga to examine their claim. Ngati Hako said that the block of land was theirs, and as previously other land had been surveyed without their permission they had taken this action. The government was criticized for paying advances on a block that had not been through the land court, and the rununga determined that although Ngati Hako had acted wrongfully, their action could be justified. When Ngati Hako refused to hand over the two accused to the authorities, the rununga claimed not to have the power to hand them over; Ngati Hako then constructed two pa to defend themselves.
Such actions provoked much frustration and criticisms of the government amongst Pakeha, but officials who investigated Ngati Hako’s complaints agreed that they had indeed lost land unjustly. Once the owners of a large domain, they had lost their land to the invading Marutuahu, whose slaves they became. When the two accused were arrested in 1882 one was found not guilty and the other was amnestied after eight months in prison because it was believed that, as rangatira, they probably had not fired the shots but had taken the responsibility for the actions of their hapu. As for McWilliams, he received what he considered inadequate compensation.
This ‘outrage’ was the first and only time in Hauraki that a Maori had shot a Pakeha, and the government’s cautious but firm response meant that the ‘peace of Hauraki’, although disturbed for a while, was maintained.

year: 2016