Biomedical subjects

Matt Lavin

Publications and source records attributed to Matt Lavin.

5 recordsLinked to original sources

PubMed2006

Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure.

Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.

Animals↗

PubMed2005

Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary.

Tertiary macrofossils of the flowering plant family Leguminosae (legumes) were used as time constraints to estimate ages of the earliest branching clades identified in separate plastid matK and rbcL gene phylogenies. Penalized likelihood rate smoothing was performed on sets of Bayesian likelihood trees generated with the AIC-selected GTR+ Gamma +I substitution model. Unequivocal legume fossils dating from the Recent continuously back to about 56 million years ago were used to fix the family stem clade at 60 million years (Ma), and at 1-Ma intervals back to 70 Ma. Specific fossils that showed distinctive combinations of apomorphic traits were used to constrain the minimum age of 12 specific internal nodes. These constraints were placed on stem rather than respective crown clades in order to bias for younger age estimates. Regardless, the mean age of the legume crown clade differs by only 1.0 to 2.5 Ma from the fixed age of the legume stem clade. Additionally, the oldest caesalpinioid, mimosoid, and papilionoid crown clades show approximately the same age range of 39 to 59 Ma. These findings all point to a rapid family-wide diversification, and predict few if any legume fossils prior to the Cenozoic. The range of the matK substitution rate, 2.1-24.6 x 10(-10) substitutions per site per year, is higher than that of rbcL, 1.6- 8.6 x 10(-10), and is accompanied by more uniform rate variation among codon positions. The matK and rbcL substitution rates are highly correlated across the legume family. For example, both loci have the slowest substitution rates among the mimosoids and the fastest rates among the millettioid legumes. This explains why groups such as the millettioids are amenable to species-level phylogenetic analysis with these loci, whereas other legume groups are not.

Bayes Theorem↗

PubMed2004

Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes.

Penalized likelihood estimated ages of both densely sampled intracontinental and sparsely sampled transcontinental crown clades in the legume family show a mostly Quaternary to Neogene age distribution. The mode ages of the intracontinental crown clades range from 4-6 Myr ago, whereas those of the transcontinental crown clades range from 8-16 Myr ago. Both of these young age estimates are detected despite methodological approaches that bias results toward older ages. Hypotheses that resort to vicariance or continental history to explain continental disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. An alternative explanation centring on dispersal that may well explain the geographical as well as the ecological phylogenetic structure of legume phylogenies is Hubbell's unified neutral theory of biodiversity and biogeography. This is the only dispersalist theory that encompasses evolutionary time and makes predictions about phylogenetic structure.

Demography↗

PubMed2004

Historical climate change and speciation: neotropical seasonally dry forest plants show patterns of both tertiary and quaternary diversification.

Historical climate changes have had a major effect on the distribution and evolution of plant species in the neotropics. What is more controversial is whether relatively recent Pleistocene climatic changes have driven speciation, or whether neotropical species diversity is more ancient. This question is addressed using evolutionary rate analysis of sequence data of nuclear ribosomal internal transcribed spacers in diverse taxa occupying neotropical seasonally dry forests, including Ruprechtia (Polygonaceae), robinioid legumes (Fabaceae), Chaetocalyx and Nissolia (Fabaceae), and Loxopterygium (Anacardiaceae). Species diversifications in these taxa occurred both during and before the Pleistocene in Central America, but were primarily pre-Pleistocene in South America. This indicates plausibility both for models that predict tropical species diversity to be recent and that invoke a role for Pleistocene climatic change, and those that consider it ancient and implicate geological factors such as the Andean orogeny and the closure of the Panama Isthmus. Cladistic vicariance analysis was attempted to identify common factors underlying evolution in these groups. In spite of the similar Mid-Miocene to Pliocene ages of the study taxa, and their high degree of endemism in the different fragments of South American dry forests, the analysis yielded equivocal, non-robust patterns of area relationships.

Base Sequence↗

PubMed2003

Heterogeneous selection on LEGCYC paralogs in relation to flower morphology and the phylogeny of Lupinus (Leguminosae).

An analysis of the molecular evolution of two LEGCYC paralogs in Lupinus (Genisteae: Leguminosae) reveals a varied history of site-specific and lineage-specific evolutionary rates and selection both within and between loci. LEGCYC genes are homologous to regulatory loci known to control floral symmetry and adaxial flower organ identity in Antirrhinum and its relatives. Within Lupinus, L. densiflorus is unusual in having flowers with a proportionally smaller standard (upright adaxial petals) and larger wings (lateral petals) than other lupin species. Phylogenetic estimates of the nonsynonymous/synonymous substitution rate ratio, omega, suggest that along the L. densiflorus lineage, positive selection (omega > 1) acted at some codon sites of one paralog, LEGCYC1B, and greater purifying selection (omega < 1) acted at some sites of the other paralog, LEGCYC1A. Overall, LEGCYC1A appears to be evolving faster than LEGCYC1B, and both paralogs are evolving faster than the internal transcribed spacer (ITS) region of nr DNA. The predominant historical pattern inferred is a highly heterogeneous "selectional mosaic" which we suggest may be typical of the teosinte branched 1-cycloidea-PCF (TCP) class of transcriptional activators, and possibly other genes. Codon models that do not account for both site-specific and lineage-specific variation in omega do not detect positive selection at these loci. We suggest a modification of existing branch-site models involving an additional omega parameter along the foreground branch, to account for the effects of both greater positive selection and greater purifying selection at different codon sites along a particular branch. The higher rates of evolution and congruent phylogenetic signal of both LEGCYC paralogs show promise for the use of these genes as markers for phylogeny reconstruction at low taxonomic levels in Genisteae [corrected]

Amino Acid Substitution↗