Molecular phylogenetics of central Canadian Physidae (Pulmonata: Basommatophora)
|
|
- Georgina Francis
- 5 years ago
- Views:
Transcription
1 10 Molecular phylogenetics of central Canadian Physidae (Pulmonata: Basommatophora) E. Pip and J.P.C. Franck Abstract: The phylogenetic relationships of four nominal south-central Canadian freshwater physids (Physa (sensu lato) skinneri Taylor, 1954, Physa integra (Haldeman, 1841), Physa gyrina (Say, 1821), and the endemic Physa winnipegensis Pip, 2004) were studied by analyses of combined partial sequences coding for mitochondrial 16S and cytochrome c oxidase (COI) genes. Maximum parsimony and neighbour joining analyses, as well as comparisons with published sequences, supported four major clades of physids, of which three are represented in central Canada. Physa skinneri and P. integra were placed within the Physa fontinalis (L., 1758) and Physa acuta Draparnaud, 1805 clades, respectively. Physa winnipegensis formed a distinct branch within the P. acuta group. An additional, previously unreported and unclassified, morph within the P. acuta group was identified from Lake Winnipeg. Résumé : Des analyses des séquences partielles combinées codant pour les gènes mitochondriaux 16S et cytochrome c oxydase (COI) nous ont permis d examiner les relations phylogénétiques de quatre espèces nominales de physidés d eau douce du centre-sud du Canada (Physa (sensu lato) skinneri Taylor, 1954, Physa integra (Haldeman, 1841), Physa gyrina (Say, 1821) et l espèce endémique Physa winnipegensis Pip, 2004). Des analyses de parcimonie maximale et du plus proche voisin et des comparaisons avec les séquences disponibles dans la littérature appuient l existence de quatre clades de physidés, dont trois sont représentés dans le centre du Canada. Physa skinneri se retrouve dans le clade de Physa fontinalis (L., 1758) et P. integra dans celui de Physa acuta Draparnaud, Physa winnipegensis forme une branche distincte du groupe de P. acuta. Nous avons identifié une forme supplémentaire, encore inédite et non classifiée, dans le groupe P. acuta provenant du lac Winnipeg. [Traduit par la Rédaction] Introduction The family Physidae encompasses a globally distributed family of sinistral freshwater snails that are particularly morphologically diversified in North America. The great variety of physical and chemical freshwater habitats occupied by members of this family, as well as environmental factors such as wide temperature ranges and predation, have contributed to the development of numerous ecophenotypes (Burnside 1998; DeWitt et al. 2000). Diversification has been further promoted by the isolation associated with island biogeography of discontiguous water bodies, particularly for organisms of limited mobility dependent on passive dispersal agents (e.g., Pip 1986; Jarne 1995), resulting in several very narrow endemics known only from a single site or a small cluster of related locations. The status of distinct species vs. conspecific ecophenotypes (as well as subspecies) within the subfamily Physinae, and the relationships among closely allied nominal species, have been the subject of much disagreement and confusion. Aside from morphological characteristics of the shell, attributes such as radular structure (e.g., Baker 1928; Clarke 1981), anatomy of the penial complex (Baker 1928; Clampitt 1970; Te 1973, 1974, 1975; Taylor 1988, 2003; Wethington Received 26 March Accepted 1 October Published on the NRC Research Press Web site at cjz.nrc.ca on 25 January E. Pip 1 and J.P.C. Franck. Department of Biology, University of Winnipeg, Winnipeg, MN R3B 2E9, Canada. 1 Corresponding author ( e.pip@uwinnipeg.ca). 2004; Wethington and Guralnick 2004), reproductive isolation (Wethington and Dillon 1997; Dillon et al. 2002, 2005; Dillon and Wethington 2004; Wethington 2004), and allozyme patterns (e.g., Te 1978; Buth and Suloway 1983; Liu 1993; Dillon and Wethington 2006) have been studied in an attempt to clarify phylogenetic relationships. However, the various individual parameters may often not be sufficiently diagnostic and may yield contradictory results when applied in combination (Te 1975; Davis 1978). Similar problems have been encountered in the pulmonate freshwater gastropod family Lymnaeidae (see Remigio and Blair 1997). A nomenclatural history of the Physidae is found in Te (1975) and Taylor (2003). Species within the subfamily Physinae have been grouped by various workers under the single genus Physa Draparnaud, 1801 for convenience and uncertainty of relationships (e.g., Clarke 1973, 1981; Te 1975), or divided into various, at times controversial, generic and subgeneric compartments (e.g., Te 1980; Bogatov and Zatravkin 1990; Remigio et al. 2001). The most comprehensive current reclassification is that of Taylor (2003), which is based on the anatomy of the male reproductive system. The latter worker recognized ~80 species grouped into 23 genera. Conversely, the discovery that different nominal species from widely separated geographic sources can interbreed under experimental conditions (e.g., Dillon et al. 2002), combined with allozyme analysis (Dillon and Wethington 2006), has supported a reduction in the number of recognized species, as well as a return to simplification of supraspecific divisions, with possibly, once again, only a single genus Physa in this subfamily (Wethington 2004). Elucidation and interpretation of inter- and intra-specific Can. J. Zool. 86: (2008) doi: /z07-112
2 Pip and Franck 11 relationships within this family need to be undertaken even as habitat destruction and degradation (Pip 2005), irreversible loss of populations, erosion of genetic diversity, and disappearance of unique gene pools proceed at an unprecendented rate (Pip 2000). The Physidae are particularly vulnerable in that significant numbers of nominal species are endemic with highly restricted areas of occurrence, for example hot springs (Clarke 1981; Te and Clarke 1985; Wethington and Guralnick 2004). Nucleotide sequencing has proven to be a practical tool for the deduction of phylogenetic relationships in gastropods (Remigio and Hebert 2003). Differences not apparent in allozymes are evident in mitochondrial DNA. Using segments of mitochondrial ribosomal 16S and cytochrome c oxidase I (COI), Remigio et al. (2001) examined the Canadian species Physella johnsoni (Clench, 1926), Physella wrighti Te and Clarke, 1985, and Physella gyrina (Say, 1821). These workers found very little or no intraspecific sequence variation for both types of segments for the individuals examined. However, interspecific differences and their relative magnitudes were apparent. A more extensive study was carried out by Wethington (2004), and Wethington and Guralnick (2004), who examined a number of species from hot and cold springs. These workers found intraspecific genetic variation, as well as varying levels of contiguity, among nominal species and recognized four primary groups of genetically related physids. In the present study, we amplified partial sequences from COI and 16S segments in four sympatric physids found in south-central Canada: Physa skinneri Taylor, 1954 (= Physa jennessi skinneri of Clarke (1973, 1981)), Physa integra (Haldeman, 1841)) (= Haitia integra of Taylor (2003)), Physella gyrina (Say, 1821), and the endemic Lake Winnipeg physid, Physa winnipegensis Pip, We also examined representatives of an additional Lake Winnipeg physid that could not be attributed to any current nominal taxon. Our objectives were to establish the relative phylogenetic positions of these central Canadian DNA sequences to published sequences for the same and other physid species from other geographical regions. Until a consensus can be reached regarding generic standings, all taxa in the present study are referred to as Physa (sensu lato). Materials and methods DNA isolation, amplification, and sequencing Individuals used in this study were field-collected in Manitoba and Alberta (Table 1). Specimens were preserved in 95% ethanol, stored at 4 8C, and analyzed within 4 months of collection. Tissue samples consisted of the tips of the foot muscles, which were microscopically examined to verify that parasites were absent. Additional tissue samples were obtained from preserved specimens at the Manitoba Museum and the University of Guelph; however, none of these proved to be amplifiable because of the degradation of the DNA. Sample preparation and sequencing analyses were performed by ATG Genetics (Vancouver, British Columbia). The preserved tissue samples were digested in proteinase K (EC ) buffer, followed by organic extraction and precipitation with ethanol. A portion of the COI mtdna gene was amplified from the total genomic DNA by polymerase chain reaction (PCR) using synthetic oligonucleotides COI(F) (defined as GGT CAA CAA ATC ATA AAG ATA TTG G) and COI(R) (defined as TAA ACT TCA GGG TGA CCA AAA AAT CA) (Folmer et al. 1994). For the 16S segment, the synthetic sequences were 16S(F) (defined as CGC CTG TTT ATC AAA AAC AT) and 16S(R) (defined as CCG GTC TGA ACT CAG ATC ACGT) (Remigio et al. 2001). The PCR products were gel-purified and sequenced on both strands with the same primers used for amplification. Sequencing was carried out using an ABI 3730 Big Dye (version 3.1) automated sequencer at the NAPS Unit, University of British Columbia, Vancouver. The forward and reverse sequences were assembled using the CAP3 sequence assembly program (Huang and Madan 1999). No gaps were encountered in the completed sequences. Sequences were deposited in GenBank with consecutive primary accession numbers EF EF for the COI sequences and EU EU for the 16S sequences (Table 1). Sequence and phylogenetic analyses The 16S and COI mtdna sequences were aligned using the default settings of Clustal X (version 1.81; Thompson et al. 1997). The sequences were aligned to previously published physid sequences; GenBank accession numbers and localities for the latter, as well as the Pseudosuccinea columella (Say, 1817) (Lymnaeidae) outgroup, are given in Table 1. The Clustal X multiple sequence alignment was imported into the GeneDoc program (Nicholas and Nicholas 1997) to manually edit nonalignable sites from the 5 and 3 ends of the alignment. Previous studies have documented the high variation in length of 16S rrna loops (Lydeard et al. 2000). The regions corresponding to the loops were deleted from the alignment, resulting in a final alignment with 878 sites. The maximum parsimony tree reconstruction was performed using PAUP (beta version 4.0*; Swofford 2001) bootstrap method heuristic search and tree bisection reconnection (TBR) branch swapping with stepwise addition and MULPARS in effect. Branches having maximum lengths of zero were collapsed to yield polytomies and no topological constraints were used. Characters were assigned equal weights. A maximum likelihood tree was constructed using the TreePuzzle program (Schmidt et al. 2002). An optimum model of substitution was chosen using the MultiPhyl webserver ( [accessed 16 January 2007]; Keane et al. 2007) with code from the ModelGenerator program (Keane et al. 2006). The model selected for the physid data set under Akaike s information criterion was the Kimura three-parameter model of base substitution with unequal base frequencies, a proportion of invariant sites, and a gamma-distributed site substitution rate (K81uf + I + G). The tree was viewed using TreeView (Page 1996). Results The physid combined 16S + COI multiple sequence alignments were phylogenetically analyzed using both maximum
3 12 Can. J. Zool. Vol. 86, 2008 Table 1. Identification labels of physid individuals and the lymnaeid outgroup species included in this study with species classification, GenBank accession number, and locality. Accession No. Identity Species COI 16S Locality MBpwin1 Physa winnipegensis EF EU Sunset Beach, Lake Winnipeg, Manitoba MBpwin2 Physa winnipegensis EF EU Sunset Beach, Lake Winnipeg, Manitoba MBpsp1 Physa sp. EF EU Sunset Beach, Lake Winnipeg, Manitoba MBpsp2 Physa sp. EF EU Sunset Beach, Lake Winnipeg, Manitoba MBpsp3 Physa sp. EF EU Victoria Beach, Lake Winnipeg, Manitoba MBpsp4 Physa sp. EF EU Sunset Beach, Lake Winnipeg, Manitoba MBpsp5 Physa sp. EF EU Sunset Beach, Lake Winnipeg, Manitoba MBpski1 Physa skinneri EF EU Ditch, southeast of Lake Winnipeg, Manitoba MBpski2 Physa skinneri EF EU Ditch, southeast of Lake Winnipeg, Manitoba MBpgy1 Physella gyrina EF EU Gull Lake, Manitoba MBpint1 Physa integra EF EU Sunset Beach, Lake Winnipeg, Manitoba ABpgy1 Physella gyrina EF NA a Lac des Arcs, Alberta wybrh2 Physa acuta AY AY Big Horn River, Wyoming pap9 Physa heterostropha AY AY Schuylkill River, Philadelphia, Pennsylvania pap10 Physa heterostropha AY AY Schuylkill River, Philadelphia, Pennsylvania argrv2 Physella virgata AY AY Gila River, Arizona cocup1 Physella cupreonitens AY AY Hot Springs, Wellesville, Colorado cocup2 Physella cupreonitens AY AY Hot Springs, Wellesville, Colorado co43906 Physella anatina AY AY Elk Creek, Garfield, Colorado co42241 Physa acuta AY AY Creek near Mesa, Colorado wyspe1 Physella spelunca AY AY Lower Kane Cave, Kane, Wyoming wyspe2 Physella spelunca AY AY Lower Kane Cave, Kane, Wyoming utznp2 Petrophysa zionis AY AY Zion National Park, Utah scysr2 Physella hendersoni AY AY Salkehatchie River, South Carolina scysr3 Physella hendersoni AY AY Salkehatchie River, South Carolina CApjon1 Physella johnsoni AY AY Middle Spring, Banff, Alberta CApjon2 Physella johnsoni AY AY Middle Spring, Banff, Alberta PjoCACOI Physella johnsoni AF AF Cave Spring, Banff, Alberta coa007 Physella gyrina AY AY Tributary of Colorado River, Grand, Colorado vacsg1 Physella gyrina AY AY Coyner Springs, Virginia vahsv2 Physella aurea AY AY Hot Springs, Virginia iobrg1 Physella gyrina AY AY Hot Springs, Virginia Nnf1 Physa fontinalis AY AY Nooredemeek, the Netherlands Nnf2 Physa fontinalis AY AY Nooredemeek, the Netherlands mi4mpcl Pseudosuccinea columella AY AY Four Mile Lake, Michigan Note: The individuals collected for this study are in boldface type. Binomens are based on those reported in GenBank. a No 16S sequence available for this sample. parsimony (MP) and maximum likelihood (ML) methodologies. Both of the tree reconstruction techniques identified four strongly supported clades, namely the Physa acuta Draparnaud, 1805, Physa pomilia Conrad, 1834, Physa fontinalis (L., 1758), and P. gyrina clades (Figs. 1A, 1B). Nodes for the four clades were robustly supported by bootstrap analyses for the MP tree and by quartet puzzling support values for the ML tree. The Lake Winnipeg P. integra (diagnosed according to shell and penial morphology) and P. winnipegensis were located within the P. acuta clade, which also included published sequences for Physella anatina Lea, 1864 (Colorado), Physa acuta (Wyoming), Physa heterostropha Say, 1816 (Pennsylvania), and Physella virgata A. Gould, 1855 (Arizona). Both the COI and 16S sequences for the two P. winnipegensis individuals (MBpwin1 and MPpwin2) were % identical and are represented as a distinct and somewhat ancestral branch that occupied an intermediate position between the hot springs species Physella cupreonitens (Cockerell, 1889) and the main body of the Physa acuta group in both tree reconstructions. However, an inconsistency was evident in the placement of co43906 (a published P. anatina sample from Colorado), which was grouped in the main body of the P. acuta group in the ML tree (Fig. 1B), but with P. winnipegensis in the MP tree (Fig. 1A). These differences originated in the 16S portion of the combined sequences; when only COI data were analyzed (not shown), P. winnipegensis occupied its own unique branch in both MP and ML tree reconstructions (as in Fig. 1B), whereas co43906 was placed in the main P. acuta group in both trees. Otherwise, trees using only COI data produced results similar to trees using the combined data. The five individuals identified as Physa sp. from Lake Winnipeg could not be assigned to a nominal species in terms of shell morphology (e.g., greater width to length ratio and a more compressed spire than in P. integra). Reproduc-
4 Pip and Franck 13 Fig. 1. Phylogenetic relationships of the Manitoba physids based on maximum parsimony (MP) and maximum likelihood (ML) analyses of the combined 16S and COI sequences. The MP tree (A) was constructed using the heuristic search method with tree bisection reconnection (TBR) branch swapping with stepwise addition. Majority rule bootstrap values based on bootstrap replicates are indicated on the major nodes. The ML tree (B) was constructed using the Kimura three-parameter model of base substitution with unequal base frequencies, a proportion of invariant sites, and a gamma-distributed site substitution rate (K81uf + I + G). The proportion of invariable sites is 0.30 and the gamma distribution alpha parameter is Base frequencies are as follows: A = 0.330, C = , G = , and T = Quartet puzzling support values generated by the TreePuzzle program are indicated at the major nodes of the tree. The taxon labels for all species included in the phylogenetic analyses are given in Table acuta clade gyrina clade fontinalis clade pomilia clade MBpsp1 MBpsp5 MBpsp4 MBpsp3 MBpsp2 pap10 wybhr2 pap9 argrv2 MBpint1 MBpwin1, MBpwin2 co43906 cocup1 cocup2 co42241 wyspe1 wyspe2 utznp2 CApjon2 CApjon1 92 coa007 PjoCACOI vacsg1 MBpgy1 vahsv2 63 iobrg1 Nnf1 Nnf2 MBpski1 MBpski2 scysr2 pomilia clade scysr3 mi4mpcl 0.1 acuta clade gyrina clade fontinalis clade scysr2 scysr3 99 MBpsp1 MBpsp5 MBpsp3 91 MBpsp2 MBpsp4 pap10 68 wybhr2 pap9 argrv2 95 co43906 MBpint1 52 MBpwin1, MBpwin2 co cocup1 cocup2 wyspe1 wyspe2 utznp2 83 CApjon1 86 CApjon2 coa007 PjoCACOI 59vacsg1 67 MBpgy1 vahsv2 iobrg1 Nnf1 Nnf2 MBpski1 MBpski2 mi4mpcl (A) 16S + COI Maximum Parsimony Tree (MP) tive anatomy (preputium with posterior gland and a unitary penial sheath) indicated an affinity with the P. acuta group. These individuals were drawn from two disjunct populations in the lake and were 98% 99% identical for both COI and 16S segments. They formed a monophyletic subclade within the P. acuta group with % and 91% bootstrap and quartet puzzling support values for the MP and ML trees, respectively. The taxa clustered in the P. gyrina clade were separated by much shorter branch lengths in both trees compared with the taxa in the P. acuta clade. The P. gyrina sampled from Manitoba (MBpgy1) clustered within a monophyletic clade in both the MP and ML trees with support values of 83% and %, respectively. Using only COI sequence data (16S data not available), the Alberta P. gyrina (ABpgy1) specimen also clustered within the P. gyrina clade in both MP and ML tree reconstructions (data not shown). This closely related group included the endemic P. johnsoni from Alberta hot springs. The physids that showed morphological and anatomical characteristics of P. skinneri (MBpski1 and MBpski2) were (B) 16S + COI Maximum Likelihood Tree (ML) assigned within the P. fontinalis clade. Both individuals were drawn from the same population and were 99% identical for both COI and 16S segments. Discussion The four major clades of P. acuta, P. gyrina, P. fontinalis, and P. pomilia identified in both the MP and ML trees were consistent with the physid phylogeny described by Wethington and Guralnick (2004). Manitoba physids were represented within the first three clades; the fourth group, represented by P. pomilia (Wethington 2004), appears to be a small group with no northern representatives identified in our survey. Physa gyrina has a wide geographical distribution in Canada (Clarke 1973, 1981; Pip 1992), as well as a very wide ecological tolerance range for water chemistry parameters (Pip 1988a). The wide distribution of this species is reflected in its morphological and molecular diversity. It is an efficient colonizer of new habitats (Pip 1986) and is the largest and most common physid in the southern parts of
5 14 Can. J. Zool. Vol. 86, 2008 the prairie provinces including Manitoba (Pip 1978, 2000). This snail is highly adaptable (Clampitt 1970; Rollo and Hawryluk 1988) and can adjust its microhabitat preferences and microdistribution to reduce interspecific competition to take advantage of optimal nutritional value of food (Pip and Stewart 1976). Like most pulmonates, it occurs primarily in shallow water, although it has been reported from depths >5 m (Pip 1991), where it harvests oxygen bubbles released by submerged macrophytes and algae (E. Pip, unpublished data). While the life span of most individuals is 1 year, some large individuals may survive longer (Pip and Stewart 1976). In the present study, the Manitoba (MBpgy1) specimen was grouped with its conspecific relatives from the US (Figs. 1A, 1B), as well as P. johnsoni from Alberta and a Physella aurea Lea, 1838 individual from Virginia. The latter two species and P. gyrina at present form an unresolved polytomy. While Te (1978), Remigio and Hebert (1998), and Lepitzki (2002) concluded on the basis of reproductive characters, allozymes, and DNA evidence that P. johnsoni is a distinct species, Taylor (2003), Wethington (2004), and Wethington and Guralnick (2004) did not recognize it as sufficiently distinct from P. gyrina. Thus, reconciliation of DNA sequence data with traditional morphological, anatomical, and biochemical parameters may require comparisons of larger or other genome sections. In central Canada, the broadest ranges of environmental chemical conditions are occupied by P. skinneri (= P. jennessi skinneri of Clarke (1973, 1981)), which can tolerate habitats with the highest values for inorganic parameters (Pip 1988a) and with the warmest temperatures (Pip 1993), although it is also common in subarctic regions (Pip 1992). This delicate species prefers habitats with minimal disturbance and is only rarely found in lakes, where it is restricted to quiet backwaters. While fossil evidence of Canadian physids is limited because of taphonomic factors that result in higher attrition rates of thin-shelled species in bottom sediments (Pip 1988b, 1990), both P. skinneri and P. gyrina are known from late-glacial deposits at least years old in southern Alberta (Harris and Pip 1973). These individuals were placed in the P. fontinalis clade (Figs. 1A, 1B). However, intraspecific variation was evident in that the two individuals drawn from the same population were not identical for either COI or 16S sequence. While Clarke (1981) confined the distribution of P. integra to the Great Lakes and St. Lawrence regions, its occurrence in Manitoba (primarily in large lakes) (Pip 1978, 2000) has been confirmed by anatomical study by D.W. Taylor (personal communication). The Lake Winnipeg individual identified as P. integra (according to reproductive anatomy) appeared in the P. acuta clade (Figs. 1A, 1B). Recent reproductive isolation studies have suggested that P. integra from the American Midwest may be able to interbreed under experimental conditions with P. heterostropha from the southeastern US and P. acuta from Europe (Dillon et al. 2002), as well as with P. virgata from the southeastern US (Dillon et al. 2005). Physa winnipegensis is a rare snail that is now known only from a few very small disjunct populations in Lake Winnipeg. Since its abundance in this lake years ago, it has suffered a catastrophic decline as habitat destruction and eutrophication of the lake have progressed; it is currently estimated at <500 individuals (E. Pip, unpublished data). This species lives on wave-lashed rocks, feeds on periphyton, and is sensitive to heavy metals (Pip 2004). The two individuals drawn from the same population were identical for both COI and 16S sequences and formed an offshoot within the P. acuta clade, suggesting common ancestry with P. anatina, P. acuta, P. heterostropha, P. virgata, and P. integra. Of these, only P. integra occurs in central Canada. The inter-relationships among these species and their taxonomic status are controversial. On the basis of anatomy, Taylor (2003) has recognized them as distinct (although he interpreted P. virgata as Physella mexicana (Philippi, 1841)), while Wethington (2004), Wethington and Guralnick (2004), Dillon et al. (2002, 2005), and Dillon and Wethington (2006) have suggested that these species should all be referred to as P. acuta. Five physid individuals (Physa sp. 1 5) (Figs. 1A, 1B) from two subpopulations in Lake Winnipeg constitute a subgroup within the P. acuta clade. These individuals could not be assigned to any current nominal species based on either shell morphology or reproductive anatomy, and may represent another undescribed taxon that is also endemic to Lake Winnipeg. Although these individuals formed a distinct subgroup, they were only 98% 99% identical for both COI and 16S. In conclusion, based on partial sequence evidence, the relationships of central Canadian physids appear to be consistent with the finding of Wethington (2004) that physids from widely separated geographical areas can be grouped into a small number of clades, composed of variously related taxa issuing from different hierarchical levels of ancestry. It is evident that varying durations of geographic and reproductive isolations, and different selective pressures, have contributed to a continuum of genetic diversity within those taxa that have wide, even transcontinental, distributions. The degree of DNA variation within and among populations of nominal taxa requires more extensive elucidation, and, as suggested by Remigio and Hebert (2003), analyses of additional genes are probably necessary to obtain a more detailed understanding of delineations at the specific level, as well as reconciliation of molecular data with morphological, anatomical, and biochemical differences. Acknowledgements Sample extraction and PCR analysis were carried out by Craig Newton at ATG Genetics and Debbie Adams at the University of British Columbia. A generous contribution by Ann Smigel through the University of Winnipeg Foundation made this study possible. References Baker, F.C The fresh water Mollusca of Wisconsin. Part I. Wis. Geol. Nat. Hist. Surv. Bull. 70. Bogatov, V.V., and Zatravkin, M.N Freshwater and brackish water gastropod molluscs of the far eastern USSR. USSR Academy of Sciences, Vladivostok. Burnside, C Ecophenotypic variation in shell morphology within the freshwater pond snail genus Physella (Pulmonata: Basommatophora) and its taxonomic implications. Ph.D. thesis, University of Texas, Arlington.
6 Pip and Franck 15 Buth, D.G., and Suloway, J.J Biochemical genetics of the snail genus Physa: a comparison of populations of two species. Malacologia, 23: Clampitt, P.T Comparative ecology of the snails Physa gyrina and Physa integra (Basommatophora: Physidae). Malacologia, 10: Clarke, A.H Freshwater molluscs of the Canadian interior basin. Malacologia, 13: PMID: Clarke, A.H The freshwater molluscs of Canada. National Museums of Canada, Ottawa, Ont. Davis, G.M Experimental methods in molluscan systematics. In Pulmonates. Edited by V. Fretter and J. Peake. Academic Press, London. pp DeWitt, T.J., Robinson, B.W., and Wilson, D.S Functional diversity among predators of a freshwater snail imposes an adaptive trade-off for shell morphology. Evol. Ecol. Res. 2: Dillon, R.T., Jr., and Wethington, A.R No-choice mating experiments among six nominal taxa of the subgenus Physella (Basommatophora: Physidae). Heldia, 6: Dillon, R.T., Jr., and Wethington, A.R The Michigan Physidae revisited: a population genetic survey. Malacologia, 48: Dillon, R.T., Jr., Wethington, A.R., Rhett, J.M., and Smith, T.P Populations of the European freshwater pulmonate Physa acuta are not reproductively isolated from American Physa heterostropha or Physa integra. Invertebr. Biol. 121: Dillon, R.T., Jr., Robinson, J.D., Smith, T.P., and Wethington, A.R No reproductive isolation between freshwater pulmonate snails Physa virgata and P. acuta. Southwest. Nat. 50: doi: / (2005)050[0415:nribfp]2.0.co;2. Folmer, O., Black, M., Hoeh, W., Lutz, R., and Vrijenhoek, R DNA primers for amplification of mitochondrial cytochrome oxidase c subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3: PMID: Harris, S.A., and Pip, E Molluscs as indicators of late- and post-glacial climatic history in Alberta. Can. J. Zool. 51: doi: /z Huang, X., and Madan, A CAP3: A DNA sequence assembly program. Genome Res. 9: doi: /gr PMID: Jarne, P Mating system, bottlenecks and genetic polymorphism in hermaphroditic animals. Genet. Res. 65: Keane, T.M., Creevey, C.J., Pentony, M.M., Naughton, T.J., and McInerney, J.O Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6: 29. doi: / PMID: Keane, T.M., Naughton, T.J., and McInerney, J.O Multi- Phyl: a high-throughput phylogenomics webserver using distributed computing. Nucleic Acids Res. 35: W33 W37. doi: /nar/gkm359. PMID: Lepitzki, A.W Resource management plan for the recovery of the Banff Springs snail (Physella johnsoni) in Banff National Park, Alberta. Report for Banff National Park, Parks Canada, Banff, Alta. Liu, H.P Diagnostic genetic loci for species in the genus Physella. Malacol. Rev. 26: 1 8. Lydeard, C., Holznagel, W.E., Schnare, M.N., and Gutell, R.R Phylogenetic analysis of molluscan mitochondrial LSU rdna sequences and secondary structures. Mol. Phylogenet. Evol. 15: doi:10.6/mpev PMID: Nicholas, K.B., and Nicholas, H.B., Jr GeneDoc: a tool for editing and annotating multiple sequence alignments. Available from [accessed 1 July 2007]. Page, R.D.M TreeView: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12: PMID: Pip, E A survey of the ecology and composition of submerged aquatic snail plant communities. Can. J. Zool. 56: doi: /z Pip, E A study of pond colonization by freshwater molluscs. J. Molluscan Stud. 52: doi: /mollus/ Pip, E. 1988a. Niche congruency of freshwater gastropods in central North America with respect to six water chemistry parameters. Nautilus, 102: Pip, E. 1988b. Differential attrition of molluscan shells in freshwater sediments. Can. J. Earth Sci. 25: Pip, E A stratigraphic study of mollusks in Lake Manitoba sediment. Walkerana, 4: Pip, E Macrophyte and associated mollusc communities in a meteor crater lake on the Precambrian Shield in Manitoba. Can. Field-Nat. 105: Pip, E The ecology of subarctic mollusks in the lower Nelson River system, Manitoba, Canada. J. Molluscan Stud. 58: doi: /mollus/ Pip, E The distribution of freshwater gastropods in central North America in relation to water temperature. Heldia, 2: Pip, E The decline of freshwater molluscs in southern Manitoba. Can. Field Nat. 114: Pip, E A new species of Physella (Gastropoda: Physidae) endemic to Lake Winnipeg, Canada. Visaya, 1: Pip, E Surface water quality in Manitoba with respect to six chemical parameters, water body and sediment type and land use. Aquat. Ecosyst. Health Manag. 8: doi: / Pip, E., and Stewart, J.M The dynamics of two aquatic plant snail associations. Can. J. Zool. 54: doi: /z Remigio, E.A., and Blair, D Molecular systematics of the freshwater snail family Lymnaeidae (Pulmonata: Basommatophora) utilising mitochondrial ribosomal DNA sequences. J. Molluscan Stud. 63: doi: /mollus/ Remigio, E.A., and Hebert, P.D.N A thermal spring endemic physid snail: mitochondrial DNA sequence evidence of a recent origin. Report for Parks Canada, Banff, Alta. Remigio, E.A., and Hebert, P.D.N Testing the utility of partial COI sequences for phylogenetic estimates of gastropod relationships. Mol. Phylogenet. Evol. 29: doi: / S (03) PMID: Remigio, E.A., Lepitzki, D.A.W., Lee, J.S., and Hebert, P.D.N Molecular systematic relationships and evidence for a recent origin of the thermal spring endemic snails Physella johnsoni and Physella wrighti (Pulmonata: Physidae). Can. J. Zool. 79: doi: /cjz Rollo, C., and Hawryluk, M Compensatory scope and resource allocation in two species of aquatic snails. Ecology, 69: doi: / Schmidt, H.A., Strimmer, K., Vingron, M., and von Haeseler, A TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18: doi: /bioinformatics/ PMID: Swofford, D.L PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0 (beta). Sinauer Associates, Inc., Sunderland, Mass.
7 16 Can. J. Zool. Vol. 86, 2008 Taylor, D.W New species of Physa (Gastropoda: Hygrophila) from the western United States. Malacol. Rev. 21: Taylor, D.W Introduction to Physidae (Gastropoda: Hygrophila): biogeography, classification, morphology. Rev. Biol. Trop. 51(Suppl. 1): PMID: Te, G.A A brief review of the systematics of the family Physidae. Malacol. Rev. 6: 61. [Abstract only.] Te, G.A Studies on Physidae (Pulmonata: Basommatophora). I. Penial complex morphological groupings. Malacol. Rev. 7: Te, G.A Michigan Physidae, with systematic notes on Physella and Physodon (Basommatophora: Pulmonata). Malacol. Rev. 8: Te, G.A A systematic study of the family Physidae (Basommatophora: Pulmonata). Ph.D. thesis, University of Michigan, Ann Arbor. Te, G.A New classification system for the family Physidae. Arch. Molluskenkd. 110: Te, G.A., and Clarke, A.H Physella (Physella) wrighti (Gastropoda: Physidae), a new species of tadpole snail from Liard Hot Springs, British Columbia. Can. Field-Nat. 99: Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: doi: / nar/ Wethington, A.R Phylogeny, taxonomy, and evolution of reproductive isolation in Physa (Pulmonata: Physidae). Ph.D. thesis, University of Alabama, Tuscaloosa. Wethington, A.R., and Dillon, R.T., Jr Selfing, outcrossing, and mixed mating in the freshwater snail Physa heterostropha: lifetime fitness and inbreeding depression. Invertebr. Biol. 116: doi: / Wethington, A.R., and Guralnick, R Are populations of physids from different hot springs distinctive lineages? Am. Malacol. Bull. 19:
A MOLECULAR PHYLOGENY OF PHYSIDAE (GASTROPODA: BASOMMATOPHORA) BASED ON MITOCHONDRIAL DNA SEQUENCES
Journal of Molluscan Studies Advance Access published 18 September 2007 A MOLECULAR PHYLOGENY OF PHYSIDAE (GASTROPODA: BASOMMATOPHORA) BASED ON MITOCHONDRIAL DNA SEQUENCES AMY R. WETHINGTON 1 AND CHARLES
More informationAlexandria C. Moore John B. Burch Thomas F. Duda Jr.
DOI 0.007/s0592-04-0645-5 RESEARCH ARTICLE Recognition of a highly restricted freshwater snail lineage (Physidae: Physella) in southeastern Oregon: convergent evolution, historical context, and conservation
More informationChapter 26 Phylogeny and the Tree of Life
Chapter 26 Phylogeny and the Tree of Life Chapter focus Shifting from the process of how evolution works to the pattern evolution produces over time. Phylogeny Phylon = tribe, geny = genesis or origin
More informationPOPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics
POPULATION GENETICS Winter 2005 Lecture 17 Molecular phylogenetics - in deriving a phylogeny our goal is simply to reconstruct the historical relationships between a group of taxa. - before we review the
More informationPHYLOGENY AND SYSTEMATICS
AP BIOLOGY EVOLUTION/HEREDITY UNIT Unit 1 Part 11 Chapter 26 Activity #15 NAME DATE PERIOD PHYLOGENY AND SYSTEMATICS PHYLOGENY Evolutionary history of species or group of related species SYSTEMATICS Study
More informationLecture 11 Friday, October 21, 2011
Lecture 11 Friday, October 21, 2011 Phylogenetic tree (phylogeny) Darwin and classification: In the Origin, Darwin said that descent from a common ancestral species could explain why the Linnaean system
More informationInDel 3-5. InDel 8-9. InDel 3-5. InDel 8-9. InDel InDel 8-9
Lecture 5 Alignment I. Introduction. For sequence data, the process of generating an alignment establishes positional homologies; that is, alignment provides the identification of homologous phylogenetic
More informationThe practice of naming and classifying organisms is called taxonomy.
Chapter 18 Key Idea: Biologists use taxonomic systems to organize their knowledge of organisms. These systems attempt to provide consistent ways to name and categorize organisms. The practice of naming
More informationIntegrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler Feb. 14, 2018. Phylogenetic trees VI: Dating in the 21st century: clocks, & calibrations;
More informationSPECIATION. REPRODUCTIVE BARRIERS PREZYGOTIC: Barriers that prevent fertilization. Habitat isolation Populations can t get together
SPECIATION Origin of new species=speciation -Process by which one species splits into two or more species, accounts for both the unity and diversity of life SPECIES BIOLOGICAL CONCEPT Population or groups
More informationDNA Barcoding Fishery Resources:
DNA Barcoding Fishery Resources: A case study in Shandong Costal Water Shufang Liu Laboratory of Molecular ecology of fishery resources Yellow Sea Fisheries Research Institute (YSFRI) Chinese Academy of
More informationDNA Barcoding and taxonomy of Glossina
DNA Barcoding and taxonomy of Glossina Dan Masiga Molecular Biology and Biotechnology Department, icipe & Johnson Ouma Trypanosomiasis Research Centre, KARI The taxonomic problem Following ~250 years of
More informationChapter 19: Taxonomy, Systematics, and Phylogeny
Chapter 19: Taxonomy, Systematics, and Phylogeny AP Curriculum Alignment Chapter 19 expands on the topics of phylogenies and cladograms, which are important to Big Idea 1. In order for students to understand
More informationChapter 8. Biogeographic Processes. Upon completion of this chapter the student will be able to:
Chapter 8 Biogeographic Processes Chapter Objectives Upon completion of this chapter the student will be able to: 1. Define the terms ecosystem, habitat, ecological niche, and community. 2. Outline how
More informationTaxonomy. Content. How to determine & classify a species. Phylogeny and evolution
Taxonomy Content Why Taxonomy? How to determine & classify a species Domains versus Kingdoms Phylogeny and evolution Why Taxonomy? Classification Arrangement in groups or taxa (taxon = group) Nomenclature
More informationEffects of Gap Open and Gap Extension Penalties
Brigham Young University BYU ScholarsArchive All Faculty Publications 200-10-01 Effects of Gap Open and Gap Extension Penalties Hyrum Carroll hyrumcarroll@gmail.com Mark J. Clement clement@cs.byu.edu See
More informationUoN, CAS, DBSC BIOL102 lecture notes by: Dr. Mustafa A. Mansi. The Phylogenetic Systematics (Phylogeny and Systematics)
- Phylogeny? - Systematics? The Phylogenetic Systematics (Phylogeny and Systematics) - Phylogenetic systematics? Connection between phylogeny and classification. - Phylogenetic systematics informs the
More information8/23/2014. Phylogeny and the Tree of Life
Phylogeny and the Tree of Life Chapter 26 Objectives Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification List the major
More informationPhylogenetic diversity and conservation
Phylogenetic diversity and conservation Dan Faith The Australian Museum Applied ecology and human dimensions in biological conservation Biota Program/ FAPESP Nov. 9-10, 2009 BioGENESIS Providing an evolutionary
More informationAmira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut
Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic analysis Phylogenetic Basics: Biological
More information(Stevens 1991) 1. morphological characters should be assumed to be quantitative unless demonstrated otherwise
Bot 421/521 PHYLOGENETIC ANALYSIS I. Origins A. Hennig 1950 (German edition) Phylogenetic Systematics 1966 B. Zimmerman (Germany, 1930 s) C. Wagner (Michigan, 1920-2000) II. Characters and character states
More informationPhylogenetic Trees. What They Are Why We Do It & How To Do It. Presented by Amy Harris Dr Brad Morantz
Phylogenetic Trees What They Are Why We Do It & How To Do It Presented by Amy Harris Dr Brad Morantz Overview What is a phylogenetic tree Why do we do it How do we do it Methods and programs Parallels
More informationCover Page. The handle holds various files of this Leiden University dissertation.
Cover Page The handle http://hdl.handle.net/1887/65602 holds various files of this Leiden University dissertation. Author: Ruchisansakun, S. Title: Balsaminaceae in Southeast Asia: systematics, evolution,
More informationDr. Amira A. AL-Hosary
Phylogenetic analysis Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University-Egypt Phylogenetic Basics: Biological
More informationTaxon: generally refers to any named group of organisms, such as species, genus, family, order, etc.. Node: represents the hypothetical ancestor
A quick review Taxon: generally refers to any named group of organisms, such as species, genus, family, order, etc.. Node: represents the hypothetical ancestor Branches: lines diverging from a node Root:
More informationIntraspecific gene genealogies: trees grafting into networks
Intraspecific gene genealogies: trees grafting into networks by David Posada & Keith A. Crandall Kessy Abarenkov Tartu, 2004 Article describes: Population genetics principles Intraspecific genetic variation
More informationDNA Sequencing as a Method for Larval Identification in Odonates
DNA Sequencing as a Method for Larval Identification in Odonates Adeline Harris 121 North St Apt 3 Farmington, ME 04938 Adeline.harris@maine.edu Christopher Stevens 147 Main St Apt 1 Farmington, ME 04938
More informationGeorgia Performance Standards for Urban Watch Restoration Field Trips
Georgia Performance Standards for Field Trips 6 th grade S6E3. Students will recognize the significant role of water in earth processes. a. Explain that a large portion of the Earth s surface is water,
More informationApplications of Genetics to Conservation Biology
Applications of Genetics to Conservation Biology Molecular Taxonomy Populations, Gene Flow, Phylogeography Relatedness - Kinship, Paternity, Individual ID Conservation Biology Population biology Physiology
More informationSpeciation. Today s OUTLINE: Mechanisms of Speciation. Mechanisms of Speciation. Geographic Models of speciation. (1) Mechanisms of Speciation
Speciation Today s OUTLINE: (1) Geographic Mechanisms of Speciation (What circumstances lead to the formation of new species?) (2) Species Concepts (How are Species Defined?) Mechanisms of Speciation Last
More informationHow to read and make phylogenetic trees Zuzana Starostová
How to read and make phylogenetic trees Zuzana Starostová How to make phylogenetic trees? Workflow: obtain DNA sequence quality check sequence alignment calculating genetic distances phylogeny estimation
More informationPhylogenies Scores for Exhaustive Maximum Likelihood and Parsimony Scores Searches
Int. J. Bioinformatics Research and Applications, Vol. x, No. x, xxxx Phylogenies Scores for Exhaustive Maximum Likelihood and s Searches Hyrum D. Carroll, Perry G. Ridge, Mark J. Clement, Quinn O. Snell
More informationWhat do we mean by a species? Morphological species concept. Morphological species concept BIOL2007 SPECIES AND BIODIVERSITY. Kanchon Dasmahapatra
BIOL2007 SPECIES AND BIODIVERSITY Kanchon Dasmahapatra What are species? How do species differ from each other? Biodiversity: How many species are there? What do we mean by a species? Darwin proved species
More informationBINF6201/8201. Molecular phylogenetic methods
BINF60/80 Molecular phylogenetic methods 0-7-06 Phylogenetics Ø According to the evolutionary theory, all life forms on this planet are related to one another by descent. Ø Traditionally, phylogenetics
More informationMicrobial Taxonomy and the Evolution of Diversity
19 Microbial Taxonomy and the Evolution of Diversity Copyright McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or display. 1 Taxonomy Introduction to Microbial Taxonomy
More informationLetter to the Editor. Department of Biology, Arizona State University
Letter to the Editor Traditional Phylogenetic Reconstruction Methods Reconstruct Shallow and Deep Evolutionary Relationships Equally Well Michael S. Rosenberg and Sudhir Kumar Department of Biology, Arizona
More informationMolecular Markers, Natural History, and Evolution
Molecular Markers, Natural History, and Evolution Second Edition JOHN C. AVISE University of Georgia Sinauer Associates, Inc. Publishers Sunderland, Massachusetts Contents PART I Background CHAPTER 1:
More informationBiology 211 (2) Week 1 KEY!
Biology 211 (2) Week 1 KEY Chapter 1 KEY FIGURES: 1.2, 1.3, 1.4, 1.5, 1.6, 1.7 VOCABULARY: Adaptation: a trait that increases the fitness Cells: a developed, system bound with a thin outer layer made of
More informationBioinformatics tools for phylogeny and visualization. Yanbin Yin
Bioinformatics tools for phylogeny and visualization Yanbin Yin 1 Homework assignment 5 1. Take the MAFFT alignment http://cys.bios.niu.edu/yyin/teach/pbb/purdue.cellwall.list.lignin.f a.aln as input and
More informationSUPPORTING INFORMATION FOR. SEquence-Enabled Reassembly of β-lactamase (SEER-LAC): a Sensitive Method for the Detection of Double-Stranded DNA
SUPPORTING INFORMATION FOR SEquence-Enabled Reassembly of β-lactamase (SEER-LAC): a Sensitive Method for the Detection of Double-Stranded DNA Aik T. Ooi, Cliff I. Stains, Indraneel Ghosh *, David J. Segal
More information4/4/2017. Extrinsic Isolating Barriers. 1. Biological species concept: 2. Phylogenetic species concept:
Chapter 13 The origin of species 13.1 What Is a Species? p. 414 Ways to identify species 1. Biological species concept: 1. There are many different concepts of species 2. Species are important taxonomic
More informationTHE NAUTILUS 123(4): , 2009 Page 282
THE NAUTILUS 123(4):282 292, 2009 Page 282 Genetic and morphological characterization of the Physidae of South Carolina (Gastropoda: Pulmonata: Basommatophora), with description of a new species Amy R.
More informationPhylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata.
Supplementary Note S2 Phylogenetic relationship among S. castellii, S. cerevisiae and C. glabrata. Phylogenetic trees reconstructed by a variety of methods from either single-copy orthologous loci (Class
More informationCorrelations to Next Generation Science Standards. Life Sciences Disciplinary Core Ideas. LS-1 From Molecules to Organisms: Structures and Processes
Correlations to Next Generation Science Standards Life Sciences Disciplinary Core Ideas LS-1 From Molecules to Organisms: Structures and Processes LS1.A Structure and Function Systems of specialized cells
More informationA Study of the Moss Parasite Eocronartium muscicola By: Alicia Knudson Advisor: Dr. Elizabeth Frieders
A Study of the Moss Parasite Eocronartium muscicola By: Alicia Knudson Advisor: Dr. Elizabeth Frieders Abstract The genus Eocronartium contains a single described species of parasitic fungus on moss plants
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationCHAPTER 10 Taxonomy and Phylogeny of Animals
CHAPTER 10 Taxonomy and Phylogeny of Animals 10-1 10-2 Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Linnaeus and Taxonomy More than 1.5 million species of
More informationHistorical Biogeography. Historical Biogeography. Systematics
Historical Biogeography I. Definitions II. Fossils: problems with fossil record why fossils are important III. Phylogeny IV. Phenetics VI. Phylogenetic Classification Disjunctions debunked: Examples VII.
More informationPost-doc fellowships to non-eu researchers FINAL REPORT. Home Institute: Centro de Investigaciones Marinas, Universidad de La Habana, CUBA
Recipient: Maickel Armenteros Almanza. Post-doc fellowships to non-eu researchers FINAL REPORT Home Institute: Centro de Investigaciones Marinas, Universidad de La Habana, CUBA Promoter: Prof. Dr. Wilfrida
More informationBig Idea #1: The process of evolution drives the diversity and unity of life
BIG IDEA! Big Idea #1: The process of evolution drives the diversity and unity of life Key Terms for this section: emigration phenotype adaptation evolution phylogenetic tree adaptive radiation fertility
More informationTaxonomy and Systematics: a broader classification system that also shows evolutionary relationships
Taxonomy: a system for naming living creatures Carrolus Linnaeus (1707-1778) The binomial system: Genus and species e.g., Macrocystis pyrifera (Giant kelp); Medialuna californiensis (halfmoon) Taxonomy
More informationa-dB. Code assigned:
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the
More informationSpeciation. Today s OUTLINE: Mechanisms of Speciation. Mechanisms of Speciation. Geographic Models of speciation. (1) Mechanisms of Speciation
Speciation Today s OUTLINE: (1) Geographic Mechanisms of Speciation (What circumstances lead to the formation of new species?) (2) Species Concepts (How are Species Defined?) Mechanisms of Speciation Last
More informationa,bD (modules 1 and 10 are required)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the
More informationConsensus methods. Strict consensus methods
Consensus methods A consensus tree is a summary of the agreement among a set of fundamental trees There are many consensus methods that differ in: 1. the kind of agreement 2. the level of agreement Consensus
More informationChapter 26. Phylogeny and the Tree of Life. Lecture Presentations by Nicole Tunbridge and Kathleen Fitzpatrick Pearson Education, Inc.
Chapter 26 Phylogeny and the Tree of Life Lecture Presentations by Nicole Tunbridge and Kathleen Fitzpatrick Investigating the Tree of Life Phylogeny is the evolutionary history of a species or group of
More informationConstructing Evolutionary/Phylogenetic Trees
Constructing Evolutionary/Phylogenetic Trees 2 broad categories: istance-based methods Ultrametric Additive: UPGMA Transformed istance Neighbor-Joining Character-based Maximum Parsimony Maximum Likelihood
More informationProject Budget: State Wildlife Grant Requested: $16,412 Project Match (UARK in kind services): $5,744 Total Project Cost: $22,156
Project Title: Genetic examination of the Ringed Crayfish species group, with special emphasis on the endemic Gapped Ringed Crayfish (Orconectes neglectus chaenodactylus) Project Summary: Morphological
More informationSpeciation. Today s OUTLINE: Mechanisms of Speciation. Mechanisms of Speciation. Geographic Models of speciation. (1) Mechanisms of Speciation
Speciation Today s OUTLINE: (1) Geographic Mechanisms of Speciation (What circumstances lead to the formation of new species?) (2) Species Concepts (How are Species Defined?) Mechanisms of Speciation Last
More informationThe Phylogenetic Reconstruction of the Grass Family (Poaceae) Using matk Gene Sequences
The Phylogenetic Reconstruction of the Grass Family (Poaceae) Using matk Gene Sequences by Hongping Liang Dissertation submitted to the Faculty of the Virginia Polytechnic Institute and State University
More informationMetacommunities Spatial Ecology of Communities
Spatial Ecology of Communities Four perspectives for multiple species Patch dynamics principles of metapopulation models (patchy pops, Levins) Mass effects principles of source-sink and rescue effects
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationPhylogenetic Analysis
Phylogenetic Analysis Aristotle Through classification, one might discover the essence and purpose of species. Nelson & Platnick (1981) Systematics and Biogeography Carl Linnaeus Swedish botanist (1700s)
More informationProcesses of Evolution
15 Processes of Evolution Forces of Evolution Concept 15.4 Selection Can Be Stabilizing, Directional, or Disruptive Natural selection can act on quantitative traits in three ways: Stabilizing selection
More informationChapter 16: Reconstructing and Using Phylogenies
Chapter Review 1. Use the phylogenetic tree shown at the right to complete the following. a. Explain how many clades are indicated: Three: (1) chimpanzee/human, (2) chimpanzee/ human/gorilla, and (3)chimpanzee/human/
More informationPGA: A Program for Genome Annotation by Comparative Analysis of. Maximum Likelihood Phylogenies of Genes and Species
PGA: A Program for Genome Annotation by Comparative Analysis of Maximum Likelihood Phylogenies of Genes and Species Paulo Bandiera-Paiva 1 and Marcelo R.S. Briones 2 1 Departmento de Informática em Saúde
More informationAnatomy of a species tree
Anatomy of a species tree T 1 Size of current and ancestral Populations (N) N Confidence in branches of species tree t/2n = 1 coalescent unit T 2 Branch lengths and divergence times of species & populations
More informationPhylogeny and systematics. Why are these disciplines important in evolutionary biology and how are they related to each other?
Phylogeny and systematics Why are these disciplines important in evolutionary biology and how are they related to each other? Phylogeny and systematics Phylogeny: the evolutionary history of a species
More informationChapter 5 Evolution of Biodiversity. Sunday, October 1, 17
Chapter 5 Evolution of Biodiversity CHAPTER INTRO: The Dung of the Devil Read and Answer Questions Provided Module 14 The Biodiversity of Earth After reading this module you should be able to understand
More informationWhat is conservation genetics? Conservation Genetics. Are genetics important in conservation? Inbreeding and loss of genetic diversity
What is conservation genetics? B242 Evolutionary Genetics Conservation Genetics Kanchon Dasmahapatra Conservation genetics is the application of genetics to preserve species as dynamic entities capable
More informationConsensus Methods. * You are only responsible for the first two
Consensus Trees * consensus trees reconcile clades from different trees * consensus is a conservative estimate of phylogeny that emphasizes points of agreement * philosophy: agreement among data sets is
More informationCHAPTERS 24-25: Evidence for Evolution and Phylogeny
CHAPTERS 24-25: Evidence for Evolution and Phylogeny 1. For each of the following, indicate how it is used as evidence of evolution by natural selection or shown as an evolutionary trend: a. Paleontology
More informationSPECIATION. SPECIATION The process by which once species splits into two or more species
SPECIATION SPECIATION The process by which once species splits into two or more species Accounts for the diversity of life on earth If no speciation, there would only be species that was continuously evolving
More informationChapter 15: Darwin and Evolution
Chapter 15: Darwin and Evolution AP Curriculum Alignment Big Idea 1 is about evolution. Charles Darwin is called the father of evolution because his theory of natural selection explains how evolution occurs.
More informationPHYLOGENY & THE TREE OF LIFE
PHYLOGENY & THE TREE OF LIFE PREFACE In this powerpoint we learn how biologists distinguish and categorize the millions of species on earth. Early we looked at the process of evolution here we look at
More informationBiogeography expands:
Biogeography expands: Phylogeography Ecobiogeography Due to advances in DNA sequencing and fingerprinting methods, historical biogeography has recently begun to integrate relationships of populations within
More informationName. Ecology & Evolutionary Biology 2245/2245W Exam 2 1 March 2014
Name 1 Ecology & Evolutionary Biology 2245/2245W Exam 2 1 March 2014 1. Use the following matrix of nucleotide sequence data and the corresponding tree to answer questions a. through h. below. (16 points)
More informationMolecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals
Project Report Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals By Shubhra Gupta CBS 598 Phylogenetic Biology and Analysis Life Science
More informationOMICS Journals are welcoming Submissions
OMICS Journals are welcoming Submissions OMICS International welcomes submissions that are original and technically so as to serve both the developing world and developed countries in the best possible
More informationSupplemental Table 1. Primers used for cloning and PCR amplification in this study
Supplemental Table 1. Primers used for cloning and PCR amplification in this study Target Gene Primer sequence NATA1 (At2g393) forward GGG GAC AAG TTT GTA CAA AAA AGC AGG CTT CAT GGC GCC TCC AAC CGC AGC
More informationPlant Names and Classification
Plant Names and Classification Science of Taxonomy Identification (necessary!!) Classification (order out of chaos!) Nomenclature (why not use common names?) Reasons NOT to use common names Theophrastus
More information"Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky
MOLECULAR PHYLOGENY "Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky EVOLUTION - theory that groups of organisms change over time so that descendeants differ structurally
More informationMiGA: The Microbial Genome Atlas
December 12 th 2017 MiGA: The Microbial Genome Atlas Jim Cole Center for Microbial Ecology Dept. of Plant, Soil & Microbial Sciences Michigan State University East Lansing, Michigan U.S.A. Where I m From
More informationPractical Bioinformatics
5/2/2017 Dictionaries d i c t i o n a r y = { A : T, T : A, G : C, C : G } d i c t i o n a r y [ G ] d i c t i o n a r y [ N ] = N d i c t i o n a r y. h a s k e y ( C ) Dictionaries g e n e t i c C o
More informationOutline. Classification of Living Things
Outline Classification of Living Things Chapter 20 Mader: Biology 8th Ed. Taxonomy Binomial System Species Identification Classification Categories Phylogenetic Trees Tracing Phylogeny Cladistic Systematics
More informationUnit 9: Evolution Guided Reading Questions (80 pts total)
Name: AP Biology Biology, Campbell and Reece, 7th Edition Adapted from chapter reading guides originally created by Lynn Miriello Unit 9: Evolution Guided Reading Questions (80 pts total) Chapter 22 Descent
More information9/19/2012. Chapter 17 Organizing Life s Diversity. Early Systems of Classification
Section 1: The History of Classification Section 2: Modern Classification Section 3: Domains and Kingdoms Click on a lesson name to select. Early Systems of Classification Biologists use a system of classification
More informationAToL: Collaborative research on ant phylogeny: a comprehensive evolutionary tree for the world s premier social organisms
AToL: Collaborative research on ant phylogeny: a comprehensive evolutionary tree for the world s premier social organisms NSF EF-0431330; 10/01/2004 09/30/2009 P.S.Ward1, Seán Brady2, Brian Fisher3 & Ted
More informationA (short) introduction to phylogenetics
A (short) introduction to phylogenetics Thibaut Jombart, Marie-Pauline Beugin MRC Centre for Outbreak Analysis and Modelling Imperial College London Genetic data analysis with PR Statistics, Millport Field
More informationTitle ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Title ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
More informationMollusca: General Characteristics
Mollusca: General Characteristics Molluscan Taxonomic Classes Polyplacophora Cephalopoda Bivalvia 7,650 sp Other 5 Classes ~1100 Gastropoda Scaphopoda Gastropoda 40,000 sp and Aplacophora Monoplacophora
More informationChapters 25 and 26. Searching for Homology. Phylogeny
Chapters 25 and 26 The Origin of Life as we know it. Phylogeny traces evolutionary history of taxa Systematics- analyzes relationships (modern and past) of organisms Figure 25.1 A gallery of fossils The
More informationTaxonomy and Biodiversity
Chapter 25/26 Taxonomy and Biodiversity Evolutionary biology The major goal of evolutionary biology is to reconstruct the history of life on earth Process: a- natural selection b- mechanisms that change
More informationA Phylogenetic Network Construction due to Constrained Recombination
A Phylogenetic Network Construction due to Constrained Recombination Mohd. Abdul Hai Zahid Research Scholar Research Supervisors: Dr. R.C. Joshi Dr. Ankush Mittal Department of Electronics and Computer
More informationLecture V Phylogeny and Systematics Dr. Kopeny
Delivered 1/30 and 2/1 Lecture V Phylogeny and Systematics Dr. Kopeny Lecture V How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics Textbook Reading: pp 425-433, 435-437
More informationHarvesting and harnessing data for biogeographical research
How do we know what grows where? Harvesting and harnessing data for biogeographical research A. Geography Tree B. Species Tree inventories and surveys natural areas, preserves, state forests, private properties
More informationAlgorithmic Methods Well-defined methodology Tree reconstruction those that are well-defined enough to be carried out by a computer. Felsenstein 2004,
Tracing the Evolution of Numerical Phylogenetics: History, Philosophy, and Significance Adam W. Ferguson Phylogenetic Systematics 26 January 2009 Inferring Phylogenies Historical endeavor Darwin- 1837
More informationTopic outline: Review: evolution and natural selection. Evolution 1. Geologic processes 2. Climate change 3. Catastrophes. Niche.
Topic outline: Review: evolution and natural selection Evolution 1. Geologic processes 2. Climate change 3. Catastrophes Niche Speciation Extinction Biodiversity Genetic engineering http://www.cengage.com/cgi-wadsworth/course_products_wp.pl?fid=m20b&product_isbn_issn=9780495015987&discipline_number=22
More informationBiology 122L Invertebrate zoology lab Molluscan diversity lab guide Author: Allison J. Gong foot radula shell visceral mass mantle cavity
Page 1 of 1 Biology 122L Invertebrate zoology lab Molluscan diversity lab guide Author: Allison J. Gong Figure source: Brusca and Brusca, 2003. Invertebrates, 2nd edition. Sinauer Associates, Inc. The
More informationBiology Assessment. Eligible Texas Essential Knowledge and Skills
Biology Assessment Eligible Texas Essential Knowledge and Skills STAAR Biology Assessment Reporting Category 1: Cell Structure and Function The student will demonstrate an understanding of biomolecules
More information