Phylogenetic position of the presumably extinct slender-billed curlew, <i>Numenius tenuirostris</i>

The high-capacity DNA analysis of museum samples opens new opportunities, associated with the investigation of extinct species evolution. Here, the complete mitochondrial genome of the presumably extinct bird species, the slender-billed curlew Numenius tenuirostris (Charadriiformes: Scolopacidae) is presented. Our results showed that mitochondrial DNA (mtDNA) is 16,705 base pairs (bp) in length and contain 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The overall base composition of the genome is 30.8% – A, 29.8% – C, 25.4% – T, 14.0% – G, and without a significant GC bias of 43.7%. Phylogenetic analyses based on the cytochrome B (cytB) gene and the whole mtDNA sequences revealed that N. tenuirostris had a close genetic relationship to Eurasian curlew (N. arquata), Far Eastern curlew (N. madagascariensis), and long-billed curlew – N. americanus. Besides, it reveals that Numenius genus is genetically distant from other Scolopacidae taxons. Together, these results provide a clear genetic perspective into the speciation process among the curlew genus members and points to a clear taxonomic position of N. tenuirostris.</p

A Venn diagram showing <i>Nasonia vitripennis</i> venom components in other Chalcidoidea species: <i>M</i>. <i>spermotrophus</i>, <i>C</i>. <i>solmsi</i>, <i>T</i>. <i>pretiosum</i> and <i>M</i>. <i>amalphitanum</i>.

A Venn diagram showing Nasonia vitripennis venom components in other Chalcidoidea species: M. spermotrophus, C. solmsi, T. pretiosum and M. amalphitanum.</p

Basic Gene Ontology (GO) analysis terms for <i>M</i>. <i>amalphitanum</i> gene products.

Basic Gene Ontology (GO) analysis terms for M. amalphitanum gene products.</p

Number of homologs of <i>N</i>. <i>vitripennis</i> venom (<i>N</i>. <i>vitripennis</i> toxin constituents) in <i>M</i>. <i>amalphitanum</i> and other Chalcidoidea species based on Universal Chalcidoidea Database [54].

Number of homologs of N. vitripennis venom (N. vitripennis toxin constituents) in M. amalphitanum and other Chalcidoidea species based on Universal Chalcidoidea Database [54].</p

Comparison of TE landscape divergence plots and TE genome fraction pie charts in four parasitoid wasp species: <i>M</i>. <i>amalphitanum</i>, <i>T</i>. <i>pretiosum</i>, <i>N</i>. <i>vitripennis</i> and <i>D</i>. <i>alloeum</i>.

Comparison of TE landscape divergence plots and TE genome fraction pie charts in four parasitoid wasp species: M. amalphitanum, T. pretiosum, N. vitripennis and D. alloeum.</p

Final statistics of the genome and transcriptome assemblies of parasitoid wasp <i>Megaphragma amalphitanum</i>.

Final statistics of the genome and transcriptome assemblies of parasitoid wasp Megaphragma amalphitanum.</p

Maximum likelihood analysis of phylogenetic relationships between Piwi/Argonaute coding sequences.

Colored dots denote sequences from T. pretiosum (blue), L. clavipes (gray), S. invicta (yellow) and M. amalphitanum (red). Recent duplications in the latter three hymenopterans are indicated by curly brackets, and the corresponding TE divergence plots from [58, 59] and Fig 3 are placed next to each curly bracket. Phylogeny analysis and notations are as in S12 Fig.</p

Size comparison of the parasitoid wasp <i>M</i>. <i>amalphitanum</i> and bacterium <i>Thiomargarita namibiensis</i>.

(A) An adult stage of the parasitoid wasp M. amalphitanum (image adapted from [5]), (B) T. namibiensis–the largest known bacterium (modified from Schulz et al. 1999) [11].</p