@article{dunn_kirby_bowern_ember_gray_mccarter_kavanagh_trautwein_nichols_gavin_et al._2024, title={Climate, climate change and the global diversity of human houses}, volume={6}, ISSN={["2513-843X"]}, DOI={10.1017/ehs.2024.5}, abstractNote={Globally, human house types are diverse, varying in shape, size, roof type, building materials, arrangement, decoration and many other features. Here we offer the first rigorous, global evaluation of the factors that influence the construction of traditional (vernacular) houses. We apply macroecological approaches to analyse data describing house features from 1900 to 1950 across 1000 societies. Geographic, social and linguistic descriptors for each society were used to test the extent to which key architectural features may be explained by the biophysical environment, social traits, house features of neighbouring societies or cultural history. We find strong evidence that some aspects of the climate shape house architecture, including floor height, wall material and roof shape. Other features, particularly ground plan, appear to also be influenced by social attributes of societies, such as whether a society is nomadic, polygynous or politically complex. Additional variation in all house features was predicted both by the practices of neighouring societies and by a society's language family. Collectively, the findings from our analyses suggest those conditions under which traditional houses offer solutions to architects seeking to reimagine houses in light of warmer, wetter or more variable climates.}, journal={EVOLUTIONARY HUMAN SCIENCES}, author={Dunn, Robert R. and Kirby, Kathryn R. and Bowern, Claire and Ember, Carol R. and Gray, Russell D. and McCarter, Joe and Kavanagh, Patrick H. and Trautwein, Michelle and Nichols, Lauren M. and Gavin, Michael C. and et al.}, year={2024}, month={Mar} }
 @article{soghigian_sither_justi_morinaga_cassel_vitek_livdahl_xia_gloria-soria_powell_et al._2023, title={Phylogenomics reveals the history of host use in mosquitoes}, volume={14}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-023-41764-y}, abstractNote={AbstractMosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: 188–250 MYA]), considerably older than previous estimates. Moreover, we utilize an extensive database of host associations for mosquitoes to show that mosquitoes have shifted to feeding upon the blood of mammals numerous times, and that mosquito diversification and host-use patterns within major lineages appear to coincide in earth history both with major continental drift events and with the diversification of vertebrate classes.}, number={1}, journal={NATURE COMMUNICATIONS}, author={Soghigian, John and Sither, Charles and Justi, Silvia Andrade and Morinaga, Gen and Cassel, Brian K. and Vitek, Christopher J. and Livdahl, Todd and Xia, Siyang and Gloria-Soria, Andrea and Powell, Jeffrey R. and et al.}, year={2023}, month={Oct} }
 @misc{frank_amato_trautwein_maia_liman_nichols_schwenk_breslin_dunn_2022, title={The evolution of sour taste}, volume={289}, ISSN={["1471-2954"]}, url={http://dx.doi.org/10.1098/rspb.2021.1918}, DOI={10.1098/rspb.2021.1918}, abstractNote={The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste—from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.}, number={1968}, journal={PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Frank, Hannah E. R. and Amato, Katie and Trautwein, Michelle and Maia, Paula and Liman, Emily R. and Nichols, Lauren M. and Schwenk, Kurt and Breslin, Paul A. S. and Dunn, Robert R.}, year={2022}, month={Feb} }
 @article{bayless_trautwein_meusemann_shin_petersen_donath_podsiadlowski_mayer_niehuis_peters_et al._2021, title={Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics}, volume={19}, ISSN={["1741-7007"]}, DOI={10.1186/s12915-020-00944-8}, abstractNote={Abstract
                Background
                The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge.
              
                Results
                Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila’s superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the ‘Modified Oviscapt Clade’ containing Tephritoidea, Nerioidea, and other families, and the ‘Cleft Pedicel Clade’ containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data.
              
                Conclusions
                Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.
              }, number={1}, journal={BMC BIOLOGY}, author={Bayless, Keith M. and Trautwein, Michelle D. and Meusemann, Karen and Shin, Seunggwan and Petersen, Malte and Donath, Alexander and Podsiadlowski, Lars and Mayer, Christoph and Niehuis, Oliver and Peters, Ralph S. and et al.}, year={2021}, month={Feb} }
 @article{li_teasdale_bayless_ellis_wiegmann_lamas_lambkin_evenhuis_nicholls_hartley_et al._2021, title={Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)}, volume={37}, ISSN={["1096-0031"]}, DOI={10.1111/cla.12436}, abstractNote={AbstractBombyliidae is a very species‐rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present‐day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the main lineages in our AHE tree to build a data set with more genes (550 loci versus 216 loci) and higher support levels. Our overall results show strong congruence with the current classification of the family, with 11 out of 14 included subfamilies recovered as monophyletic. Heterotropinae and Mythicomyiinae are successive sister groups to the remainder of the family. We examined the evolution of key morphological characters through our phylogenetic hypotheses and show that neither the “sand chamber subfamilies” nor the “Tomophthalmae” are monophyletic in our phylogenomic analyses. Based on our results, we reinstate two tribes at the subfamily level (Phthiriinae stat. rev. and Ecliminae stat. rev.) and we include the genus Sericosoma Macquart (previously incertae sedis) in the subfamily Oniromyiinae, bringing the total number of bee fly subfamilies to 19. Our dating analyses indicate a Jurassic origin of the family (165–194 Ma), with the sand chamber evolving early in bee fly evolution, in the late Jurassic or mid‐Cretaceous (100–165 Ma). We hypothesize that the angiosperm radiation and the hothouse climate established during the late Cretaceous accelerated the diversification of bee flies, by providing an expanded range of resources for the parasitoid larvae and nectarivorous adults.}, number={3}, journal={CLADISTICS}, author={Li, Xuankun and Teasdale, Luisa C. and Bayless, Keith M. and Ellis, Allan G. and Wiegmann, Brian M. and Lamas, Carlos Jose E. and Lambkin, Christine L. and Evenhuis, Neal L. and Nicholls, James A. and Hartley, Diana and et al.}, year={2021}, month={Jun}, pages={276–297} }
 @article{thoemmes_fergus_urban_trautwein_dunn_2014, title={Ubiquity and Diversity of Human-Associated Demodex Mites}, volume={9}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84925470906&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0106265}, abstractNote={Demodex mites are a group of hair follicle and sebaceous gland-dwelling species. The species of these mites found on humans are arguably the animals with which we have the most intimate interactions. Yet, their prevalence and diversity have been poorly explored. Here we use a new molecular method to assess the occurrence of Demodex mites on humans. In addition, we use the 18S rRNA gene (18S rDNA) to assess the genetic diversity and evolutionary history of Demodex lineages. Within our samples, 100% of people over 18 years of age appear to host at least one Demodex species, suggesting that Demodex mites may be universal associates of adult humans. A phylogenetic analysis of 18S rDNA reveals intraspecific structure within one of the two named human-associated Demodex species, D. brevis. The D. brevis clade is geographically structured, suggesting that new lineages are likely to be discovered as humans from additional geographic regions are sampled.}, number={8}, journal={PLOS ONE}, author={Thoemmes, Megan S. and Fergus, Daniel J. and Urban, Julie and Trautwein, Michelle and Dunn, Robert R.}, year={2014}, month={Aug} }
 @article{gavin_botero_bowern_colwell_dunn_dunn_gray_kirby_mccarter_powell_et al._2013, title={Toward a Mechanistic Understanding of Linguistic Diversity}, volume={63}, ISSN={["1525-3244"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84881490978&partnerID=MN8TOARS}, DOI={10.1525/bio.2013.63.7.6}, abstractNote={Our species displays remarkable linguistic diversity. Although the uneven distribution of this diversity demands explanation, the drivers of these patterns have not been conclusively determined. We address this issue in two steps: First, we review previous empirical studies whose authors have suggested environmental, geographical, and sociocultural drivers of linguistic diversification. However, contradictory results and methodological variation make it difficult to draw general conclusions. Second, we outline a program for future research. We suggest that future analyses should account for interactions among causal factors, the lack of spatial and phylogenetic independence of the data, and transitory patterns. Recent analytical advances in biogeography and evolutionary biology, such as simulation modeling of diversity patterns, hold promise for testing four key mechanisms of language diversification proposed here: neutral change, population movement, contact, and selection. Future modeling approaches should also evaluate how the outcomes of these processes are influenced by demography, environmental heterogeneity, and time.}, number={7}, journal={BIOSCIENCE}, author={Gavin, Michael C. and Botero, Carlos A. and Bowern, Claire and Colwell, Robert K. and Dunn, Michael and Dunn, Robert R. and Gray, Russell D. and Kirby, Kathryn R. and McCarter, Joe and Powell, Adam and et al.}, year={2013}, month={Jul}, pages={524–535} }
 @article{lucky_trautwein_guenard_weiser_dunn_2013, title={Tracing the Rise of Ants - Out of the Ground}, volume={8}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84891337406&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0084012}, abstractNote={The evolution of ants (Hymenoptera: Formicidae) is increasingly well-understood due to recent phylogenetic analyses, along with estimates of divergence times and diversification rates. Yet, leading hypotheses regarding the ancestral habitat of ants conflict with new findings that early ant lineages are cryptic and subterranean. Where the ants evolved, in respect to habitat, and how habitat shifts took place over time have not been formally tested. Here, we reconstruct the habitat transitions of crown-group ants through time, focusing on where they nest and forage (in the canopy, litter, or soil). Based on ancestral character reconstructions, we show that in contrast to the current consensus based on verbal arguments that ants evolved in tropical leaf litter, the soil is supported as the ancestral stratum of all ants. We also find subsequent movements up into the litter and, in some cases, into the canopy. Given the global importance of ants, because of their diversity, ecological influence and status as the most successful eusocial lineage on Earth, understanding the early evolution of this lineage provides insight into the factors that made this group so successful today.}, number={12}, journal={PLOS ONE}, author={Lucky, Andrea and Trautwein, Michelle D. and Guenard, Benoit S. and Weiser, Michael D. and Dunn, Robert R.}, year={2013}, month={Dec} }
 @misc{yeates_cameron_trautwein_2012, title={A view from the edge of the forest: recent progress in understanding the relationships of the insect orders}, volume={51}, ISSN={["1440-6055"]}, DOI={10.1111/j.1440-6055.2012.00857.x}, abstractNote={AbstractResearch over the last two decades has significantly increased our understanding of the evolutionary position of the insects among other arthropods, and the relationships among the insect Orders. Many of these insights have been established through increasingly sophisticated analyses of DNA sequence data from a limited number of genes. Recent results have established the relationships of the Holometabola, but relationships among the hemimetabolous orders have been more difficult to elucidate. A strong consensus on the relationships among the Palaeoptera (Ephemeroptera and Odonata) and their relationship to the Neoptera has not emerged with all three possible resolutions supported by different data sets. While polyneopteran relationships generally have resisted significant resolution, it is now clear that termites, Isoptera, are nested within the cockroaches, Blattodea. The newly discovered order Mantophasmatodea is difficult to place with the balance of studies favouring Grylloblattodea as sister‐group. While some studies have found the paraneopteran orders (Hemiptera, Thysanoptera, Phthiraptera and Psocoptera) monophyletic, evidence suggests that parasitic lice (Phthiraptera) have evolved from groups within the book and bark lice (Psocoptera), and may represent parallel evolutions of parasitism within two major louse groups. Within Holometabola, it is now clear that Hymenoptera are the sister to the other orders, that, in turn are divided into two clades, the Neuropteroidea (Coleoptera, Neuroptera and relatives) and the Mecopterida (Trichoptera, Lepidoptera, Diptera and their relatives). The enigmatic order Strepsiptera, the twisted wing insects, have now been placed firmly near Coleoptera, rejecting their close relationship to Diptera that was proposed some 15 years ago primarily based on ribosomal DNA data. Phylogenomic‐scale analyses are just beginning to be focused on the relationships of the insect orders, and this is where we expect to see resolution of palaeopteran and polyneopteran relationships. Future research will benefit from greater coordination between intra and inter‐ordinal analyses. This will maximise the opportunities for appropriate outgroup choice at the intraordinal level and provide the background knowledge for the interordinal analyses to span the maximum phylogenetic scope within groups.}, journal={AUSTRALIAN JOURNAL OF ENTOMOLOGY}, author={Yeates, David K. and Cameron, Stephen L. and Trautwein, Michelle}, year={2012}, month={May}, pages={79–87} }
 @article{trautwein_wiegmann_beutel_kjer_yeates_2012, title={Advances in Insect Phylogeny at the Dawn of the Postgenomic Era}, volume={57}, ISSN={["1545-4487"]}, DOI={10.1146/annurev-ento-120710-100538}, abstractNote={Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).}, journal={ANNUAL REVIEW OF ENTOMOLOGY, VOL 57}, author={Trautwein, Michelle D. and Wiegmann, Brian M. and Beutel, Rolf and Kjer, Karl M. and Yeates, David K.}, year={2012}, pages={449-+} }
 @article{wiegmann_trautwein_winkler_barr_kim_lambkin_bertone_cassel_bayless_heimberg_et al._2011, title={Episodic radiations in the fly tree of life}, volume={108}, number={14}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Wiegmann, B. M. and Trautwein, M. D. and Winkler, I. S. and Barr, N. B. and Kim, J. W. and Lambkin, C. and Bertone, M. A. and Cassel, B. K. and Bayless, K. M. and Heimberg, A. M. and et al.}, year={2011}, pages={5690–5695} }
 @article{trautwein_wiegmann_yeates_2010, title={A multigene phylogeny of the fly superfamily Asiloidea (Insecta): Taxon sampling and additional genes reveal the sister-group to all higher flies (Cyclorrhapha)}, volume={56}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2010.04.017}, abstractNote={Asiloidea are a group of 9 lower brachyceran fly families, considered to be the closest relative to the large Metazoan radiation Eremoneura (Cyclorrhapha+Empidoidea). The evidence for asiloid monophyly is limited, and few characters define the relationships between the families of Asiloidea and Eremoneura. Additionally, enigmatic genera, Hilarimorpha and Apystomyia, retain morphological characters of both asiloids and higher flies. We use the nuclear protein-coding gene CAD and 28S rDNA to test the monophyly of Asiloidea and to resolve its relationship to Eremoneura. We explore the effects of taxon sampling on support values and topological stability, the resolving power of additional genes, and hypothesis testing using four-cluster likelihood mapping. We find that: (1) the 'asiloid' genus Apystomyia is sister to Cyclorrhapha, (2) the remaining asiloids are monophyletic at the exclusion of the family Bombyliidae, and (3) our best estimate of relationships places the asiloid flies excluding Bombyliidae as the sister-group to Eremoneura, though high support is lacking.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Trautwein, Michelle D. and Wiegmann, Brian M. and Yeates, David K.}, year={2010}, month={Sep}, pages={918–930} }
 @article{wiegmann_trautwein_kim_cassel_bertone_winterton_yeates_2009, title={Single-copy nuclear genes resolve the phylogeny of the holometabolous insects}, volume={7}, ISSN={["1741-7007"]}, DOI={10.1186/1741-7007-7-34}, abstractNote={Evolutionary relationships among the 11 extant orders of insects that undergo complete metamorphosis, called Holometabola, remain either unresolved or contentious, but are extremely important as a context for accurate comparative biology of insect model organisms. The most phylogenetically enigmatic holometabolan insects are Strepsiptera or twisted wing parasites, whose evolutionary relationship to any other insect order is unconfirmed. They have been controversially proposed as the closest relatives of the flies, based on rDNA, and a possible homeotic transformation in the common ancestor of both groups that would make the reduced forewings of Strepsiptera homologous to the reduced hindwings of Diptera. Here we present evidence from nucleotide sequences of six single-copy nuclear protein coding genes used to reconstruct phylogenetic relationships and estimate evolutionary divergence times for all holometabolan orders.Our results strongly support Hymenoptera as the earliest branching holometabolan lineage, the monophyly of the extant orders, including the fleas, and traditionally recognized groupings of Neuropteroidea and Mecopterida. Most significantly, we find strong support for a close relationship between Coleoptera (beetles) and Strepsiptera, a previously proposed, but analytically controversial relationship. Exploratory analyses reveal that this relationship cannot be explained by long-branch attraction or other systematic biases. Bayesian divergence times analysis, with reference to specific fossil constraints, places the origin of Holometabola in the Carboniferous (355 Ma), a date significantly older than previous paleontological and morphological phylogenetic reconstructions. The origin and diversification of most extant insect orders began in the Triassic, but flourished in the Jurassic, with multiple adaptive radiations producing the astounding diversity of insect species for which these groups are so well known.These findings provide the most complete evolutionary framework for future comparative studies on holometabolous model organisms and contribute strong evidence for the resolution of the 'Strepsiptera problem', a long-standing and hotly debated issue in insect phylogenetics.}, journal={BMC BIOLOGY}, author={Wiegmann, Brian M. and Trautwein, Michelle D. and Kim, Jung-Wook and Cassel, Brian K. and Bertone, Matthew A. and Winterton, Shaun L. and Yeates, David K.}, year={2009}, month={Jun} }