A phylogenetic tree comprising clades with high bootstrap values or other strong measures of stat... more A phylogenetic tree comprising clades with high bootstrap values or other strong measures of statistical support is usually interpreted as providing a good estimate of the true phylogeny. Convergent evolution acting on groups of characters in concert, however, can lead to highly supported but erroneous phylogenies. Identifying such groups of phylogenetically misleading characters is obviously desirable. Here we present a procedure that uses an independent data source to identify sets of characters that have undergone concerted convergent evolution. We examine the problematic case of the cormorants and shags, for which trees constructed using osteological and molecular characters both have strong statistical support and yet are fundamentally incongruent. We find that the osteological characters can be separated into those that fit the phylogenetic history implied by the molecular data set and those that do not. Moreover, these latter nonfitting osteological characters are internally consistent and form groups of mutually compatible characters or "cliques," which are significantly larger than cliques of shuffled characters. We suggest, therefore, that these cliques of characters are the result of similar selective pressures and are a signature of concerted convergence.
The aptly named microcormorants (currently placed in the genus Microcarbo) form a morphologically... more The aptly named microcormorants (currently placed in the genus Microcarbo) form a morphologically diminutive and distinct clade sister to all other living cormorants and shags. However, the relationships within Microcarbo are largely speculative. Sequence data resolve these relationships unambiguously, with our phylogeny suggesting that the microcormorants separated from the other cormorants ~16 Mya and showing that the two African species [the reed (or long-tailed) cormorant, Microcarbo africanus, and the crowned cormorant, Microcarbo coronatus] are closely related sister taxa, forming a clade that diverged from the other microcormorants ~12 Mya. The deep split between the African microcormorants and the others is considerably older than many well-recognized generic splits within the cormorants (e.g. Leucocarbo and Phalacrocorax). Thus, we suggest that the African microcormorants warrant their own genus, and we erect Afrocarbo, with type species Pelecanus africanus. Within the redu...
Details are provided on 16 land snail genera, eight freshwater molluscan species, one estuarine s... more Details are provided on 16 land snail genera, eight freshwater molluscan species, one estuarine species, 47 land snail species and varieties from New Zealand, and a further three land snail species putatively from New Zealand, which were described by Frederick Wollaston Hutton between 1879 and 1904. Original primary type material of 54 species was located during the present study. Lectotypes are designated for: Amphidoxa cornea Hutton, 1882, Amphidoxa jacquenetta Hutton, 1883, Amphidoxa perdita Hutton, 1883, Charopa cassandra Hutton, 1883, Cyclotus charmian Hutton, 1883, Fruticicola adriana Hutton, 1883, Gerontia cordelia Hutton, 1883, Gerontia pantherina Hutton, 1882, Microphysa pumila Hutton, 1882, Patula jessica Hutton, 1883, Patula lucetta Hutton, 1884, Patula sylvia Hutton, 1883, Patula tapirina Hutton, 1882, Pfeifferia cressida Hutton, 1883, Phrixgnathus celia Hutton, 1883, Phrixgnathus haasti Hutton, 1883, Phrixgnathus marginatus Hutton, 1882, Phrixgnathus phrynia Hutton, 188...
The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever... more The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and super-families. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (Phyllostomoi-dea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffen-bach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mys-tacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoi-dea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous– Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctili-onoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.
A model of patch choice, in which individuals choose between two sites with different continuous ... more A model of patch choice, in which individuals choose between two sites with different continuous input rates, is presented. Individuals differ in their competitive ability and may not perceive small resource differences between these patches. The model is historical, in that the individuals are added to the system sequentially, building up a complete system. Including this historical aspect leads to a different result from that derived using equilibrium-centred models. Monte Carlo simulations of the model show that (1) the historical development of a distribution of animals significantly affects its final form, and (2) an equilibrium distribution may not be reached until long after all individuals are present. When individuals have different competitive abilities, the 'free' assumption of the ideal free distribution (IFD) is violated, giving rise to a distribution we call the ideal competitive-differences distribution (ICDD). As has been previously noted, several different ICDD outcomes are possible in a given situation, but our historical perspective suggests that deviations from the habitat-matching prediction of the IFD (usually undermatchings) are much more likely than previously realized. A widely cited example of the ICDD, for instance, fails to give the IFD-mimicking habitat-matching distribution as its most likely outcome. Lastly, perceptual limits in conjunction with competitive differences result in mismatches with the ICDD. It is suggested, therefore, that experimental results are likely to undermatch resources compared with predictions from both the IFD and the ICDD.
The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever... more The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.
New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups ... more New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal coordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades. Citation: Rawlence NJ, Till CE, Scofield RP, Tennyson AJD, Collins CJ, et al. (2014) Strong Phylogeographic Structure in a Sedentary Seabird, the Stewart Island Shag (Leucocarbo chalconotus). PLoS ONE 9(3): e90769.
Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic m... more Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic methods; it is frequently invoked post hoc, upon recovering a different tree from the one expected based on prior evidence. We demonstrate that methods that do not force the data onto a single tree, such as spectral analysis, Neighbor-Net, and consensus networks, can be used to detect conflicting signals within the data, including those caused by long-branch attraction. We illustrate this approach using a set of taxa from three unambiguously monophyletic families within the Pelecaniformes: the darters, the cormorants and shags, and the gannets and boobies. These three families are universally acknowledged as forming a monophyletic group, but the relationship between the families remains contentious. Using sequence data from three mitochondrial genes (12S, ATPase 6, and ATPase 8) we demonstrate that the relationship between these three families is difficult to resolve because they are separated by a short internal branch and there are conflicting signals due to long-branch attraction, which are confounded with nonhomogeneous sequence evolution across the different genes. Spectral analysis, Neighbor-Net, and consensus networks reveal conflicting signals regarding the placement of one of the darters, with support found for darter monophyly, but also support for a conflicting grouping with the outgroup, pelicans. Furthermore, parsimony and maximum-likelihood analyses produced different trees, with one of the two most parsimonious trees not supporting the monophyly of the darters. Monte Carlo simulations, however, were not sensitive enough to reveal long-branch attraction unless the branches are longer than those actually observed. These results indicate that spectral analysis, Neighbor-Net, and consensus networks offer a powerful approach to detecting and understanding the source of conflicting signals within phylogenetic data. [Anhingidae; consensus networks; darters; long-branch attraction; Neighbor-Net; Pelecaniformes; spectral analysis.]
A phylogenetic tree comprising clades with high bootstrap values or other strong measures of stat... more A phylogenetic tree comprising clades with high bootstrap values or other strong measures of statistical support is usually interpreted as providing a good estimate of the true phylogeny. Convergent evolution acting on groups of characters in concert, however, can lead to highly supported but erroneous phylogenies. Identifying such groups of phylogenetically misleading characters is obviously desirable. Here we present a procedure that uses an independent data source to identify sets of characters that have undergone concerted convergent evolution. We examine the problematic case of the cormorants and shags, for which trees constructed using osteological and molecular characters both have strong statistical support and yet are fundamentally incongruent. We find that the osteological characters can be separated into those that fit the phylogenetic history implied by the molecular data set and those that do not. Moreover, these latter nonfitting osteological characters are internally consistent and form groups of mutually compatible characters or "cliques," which are significantly larger than cliques of shuffled characters. We suggest, therefore, that these cliques of characters are the result of similar selective pressures and are a signature of concerted convergence.
The aptly named microcormorants (currently placed in the genus Microcarbo) form a morphologically... more The aptly named microcormorants (currently placed in the genus Microcarbo) form a morphologically diminutive and distinct clade sister to all other living cormorants and shags. However, the relationships within Microcarbo are largely speculative. Sequence data resolve these relationships unambiguously, with our phylogeny suggesting that the microcormorants separated from the other cormorants ~16 Mya and showing that the two African species [the reed (or long-tailed) cormorant, Microcarbo africanus, and the crowned cormorant, Microcarbo coronatus] are closely related sister taxa, forming a clade that diverged from the other microcormorants ~12 Mya. The deep split between the African microcormorants and the others is considerably older than many well-recognized generic splits within the cormorants (e.g. Leucocarbo and Phalacrocorax). Thus, we suggest that the African microcormorants warrant their own genus, and we erect Afrocarbo, with type species Pelecanus africanus. Within the redu...
Details are provided on 16 land snail genera, eight freshwater molluscan species, one estuarine s... more Details are provided on 16 land snail genera, eight freshwater molluscan species, one estuarine species, 47 land snail species and varieties from New Zealand, and a further three land snail species putatively from New Zealand, which were described by Frederick Wollaston Hutton between 1879 and 1904. Original primary type material of 54 species was located during the present study. Lectotypes are designated for: Amphidoxa cornea Hutton, 1882, Amphidoxa jacquenetta Hutton, 1883, Amphidoxa perdita Hutton, 1883, Charopa cassandra Hutton, 1883, Cyclotus charmian Hutton, 1883, Fruticicola adriana Hutton, 1883, Gerontia cordelia Hutton, 1883, Gerontia pantherina Hutton, 1882, Microphysa pumila Hutton, 1882, Patula jessica Hutton, 1883, Patula lucetta Hutton, 1884, Patula sylvia Hutton, 1883, Patula tapirina Hutton, 1882, Pfeifferia cressida Hutton, 1883, Phrixgnathus celia Hutton, 1883, Phrixgnathus haasti Hutton, 1883, Phrixgnathus marginatus Hutton, 1882, Phrixgnathus phrynia Hutton, 188...
The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever... more The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and super-families. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (Phyllostomoi-dea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffen-bach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mys-tacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoi-dea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous– Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctili-onoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.
A model of patch choice, in which individuals choose between two sites with different continuous ... more A model of patch choice, in which individuals choose between two sites with different continuous input rates, is presented. Individuals differ in their competitive ability and may not perceive small resource differences between these patches. The model is historical, in that the individuals are added to the system sequentially, building up a complete system. Including this historical aspect leads to a different result from that derived using equilibrium-centred models. Monte Carlo simulations of the model show that (1) the historical development of a distribution of animals significantly affects its final form, and (2) an equilibrium distribution may not be reached until long after all individuals are present. When individuals have different competitive abilities, the 'free' assumption of the ideal free distribution (IFD) is violated, giving rise to a distribution we call the ideal competitive-differences distribution (ICDD). As has been previously noted, several different ICDD outcomes are possible in a given situation, but our historical perspective suggests that deviations from the habitat-matching prediction of the IFD (usually undermatchings) are much more likely than previously realized. A widely cited example of the ICDD, for instance, fails to give the IFD-mimicking habitat-matching distribution as its most likely outcome. Lastly, perceptual limits in conjunction with competitive differences result in mismatches with the ICDD. It is suggested, therefore, that experimental results are likely to undermatch resources compared with predictions from both the IFD and the ICDD.
The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever... more The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.
New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups ... more New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal coordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades. Citation: Rawlence NJ, Till CE, Scofield RP, Tennyson AJD, Collins CJ, et al. (2014) Strong Phylogeographic Structure in a Sedentary Seabird, the Stewart Island Shag (Leucocarbo chalconotus). PLoS ONE 9(3): e90769.
Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic m... more Long-branch attraction is a well-known source of systematic error that can mislead phylogenetic methods; it is frequently invoked post hoc, upon recovering a different tree from the one expected based on prior evidence. We demonstrate that methods that do not force the data onto a single tree, such as spectral analysis, Neighbor-Net, and consensus networks, can be used to detect conflicting signals within the data, including those caused by long-branch attraction. We illustrate this approach using a set of taxa from three unambiguously monophyletic families within the Pelecaniformes: the darters, the cormorants and shags, and the gannets and boobies. These three families are universally acknowledged as forming a monophyletic group, but the relationship between the families remains contentious. Using sequence data from three mitochondrial genes (12S, ATPase 6, and ATPase 8) we demonstrate that the relationship between these three families is difficult to resolve because they are separated by a short internal branch and there are conflicting signals due to long-branch attraction, which are confounded with nonhomogeneous sequence evolution across the different genes. Spectral analysis, Neighbor-Net, and consensus networks reveal conflicting signals regarding the placement of one of the darters, with support found for darter monophyly, but also support for a conflicting grouping with the outgroup, pelicans. Furthermore, parsimony and maximum-likelihood analyses produced different trees, with one of the two most parsimonious trees not supporting the monophyly of the darters. Monte Carlo simulations, however, were not sensitive enough to reveal long-branch attraction unless the branches are longer than those actually observed. These results indicate that spectral analysis, Neighbor-Net, and consensus networks offer a powerful approach to detecting and understanding the source of conflicting signals within phylogenetic data. [Anhingidae; consensus networks; darters; long-branch attraction; Neighbor-Net; Pelecaniformes; spectral analysis.]
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