02250nas a2200277 4500008004100000245008100041210006900122300001000191490000800201520140800209653001401617653001901631653001601650653001401666653002701680653002101707653002901728100002401757700002401781700001901805700002101824700001701845700002301862700002101885856006601906 2004 eng d00aParasite escape mechanisms drive morphological diversification in avian lice0 aParasite escape mechanisms drive morphological diversification i a12 pp0 v2913 a

Organisms that have repeatedly evolved similar morphologies owing to the same selective pressures provide excellent cases in which to examine specific morphological changes and their relevance to the ecology and evolution of taxa. Hosts of permanent parasites act as an independent evolutionary experiment, as parasites on these hosts are thought to be undergoing similar selective pressures. Parasitic feather lice have repeatedly diversified into convergent ecomorphs in different microhabitats on their avian hosts. We quantified specific morphological characters to determine (i) which traits are associated with each ecomorph, (ii) the quantitative differences between these ecomorphs, and (iii) if there is evidence of displacement among co-occurring lice as might be expected under louse–louse competition on the host. We used nano-computed tomography scan data of 89 specimens, belonging to four repeatedly evolved ecomorphs, to examine their mandibular muscle volume, limb length and three-dimensional head shape data. Here, we find evidence that lice repeatedly evolve similar morphologies as a mechanism to escape host defences, but also diverge into different ecomorphs related to the way they escape these defences. Lice that co-occur with other genera on a host exhibit greater morphological divergence, indicating a potential role of competition in evolutionary divergence.

10aBird lice10aco-adaptations10aCT scanning10aEvolution10aGuimaraesiella antiqua10amicro-morphology10aNeopsittaconirmus bushae1 aKOLENCIK, STANISLAV1 aStanley, Edward, L.1 aPunnath, Aswaj1 aGrant, Avery, R.1 aDoña, Jorge1 aJohnson, Kevin, P.1 aAllen, Julie, M. uhttps://royalsocietypublishing.org/doi/10.1098/rspb.2023.266502986nas a2200277 4500008004100000022001400041245006400055210006400119260001200183300001400195490000700209520217200216653001502388653002002403653002202423653002602445653002802471100001602499700001802515700002102533700001402554700002102568700001802589700002002607856008102627 2019 eng d a2041-210X00aPhylogenomics from low‐coverage whole‐genome sequencing0 aPhylogenomics from low‐coverage whole‐genome sequencing c04-2019 a507 - 5170 v103 a

1.Phylogenetic studies are increasingly reliant on next‐generation sequencing (NGS). Transcriptomic and hybrid‐enrichment sequencing techniques remain the most prevalent methods for phylogenomic data collection due to their relatively low demands for computing powers and sequencing prices, compared to whole genome shotgun sequencing (WGS). However, the transcriptome‐based method is constrained by the availability of fresh materials and hybrid enrichment is limited by genomic resources necessary in probe designs, especially for non‐model organisms.

2. We present a novel WGS‐based pipeline for extracting essential phylogenomic markers through rapid de novo genome assembling from low‐coverage genome data, employing a series of computationally efficient bioinformatic tools. We tested the pipeline on a Hexapoda dataset and a more focused Phthiraptera dataset (genome sizes 0.1–2 Gbp), and further investigated the effects of sequencing depth on target assembly success rate based on raw data of six insect genomes (0.1–1 Gbp).

3. Each genome assembly was completed in 2–24 hours on desktop PCs. We extracted 872–1,615 near‐universal single‐copy orthologs (BUSCOs) per species. This method also enables development of ultraconserved element (UCE) probe sets; we generated probes for Phthiraptera based on our WGS assemblies, containing 55,030 baits targeting 2,832 loci, from which we extracted 2,125–2,272 UCEs. Resulting phylogenetic trees all agreed with currently‐accepted topologies, indicating that markers produced in our methods were valid for phylogenomic studies. We also showed that 10–20× sequencing coverage was sufficient to produce hundreds to thousands of targeted loci from BUSCO sets, and even lower coverage (5×) was required for UCEs.

4. Our study demonstrates the feasibility of conducting phylogenomics from low‐coverage WGS for a wide range of organisms without reference genomes. This new approach has major advantages in data collection, particularly in reducing sequencing cost and computing consumption, while expanding loci choices.

10adesktop PC10agenome assembly10ahybrid enrichment10asingle-copy orthologs10aultraconserved elements1 aZhang, Feng1 aDing, Yinhuan1 aZhu, Chao‐Dong1 aZhou, Xin1 aOrr, Michael, C.1 aScheu, Stefan1 aLuan, Yun‐Xia uhttps://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.1314500394nam a2200121 4500008004100000245002700041210002500068260006900093300000800162490000700170100002100177856007400198 1980 eng d00aPhthiraptera (Insecta)0 aPhthiraptera Insecta aJohannesburgbSouth African Institute for Medical Researchc1980 a3270 vIV1 aLedger, John, A. uhttp://www.phthiraptera.info/sites/phthiraptera.info/files/0521-2.pdf