Cryptic diversity within three South American whip spider species (Arachnida, Amblypygi)

Machine learning approaches delimit cryptic taxa in a previously intractable species complex

Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.

Variations in the carapace shape of whip spiders (Arachnida: Amblypygi)

Morphological studies often need to reference body size to correctly characterise the shape of organisms. In arthropods, the most commonly used reference for this is the length or width of the carapace, thorax, or the prosoma in the case of chelicerates. However, in the case of animals with unlimited growth, such as whip spiders, this measure could be irrelevant if growth is allometric. In this study, we analyse the ontogenetic modifications in prosoma outline shape in whip spiders during growth and compare the differences in shape between species. Differences are important for the relative prosoma width between species and, in the case of Damon medius, during growth in the juvenile stages, whereas the shape remains stable in mature stages. We conclude that a one-dimensional measure (i.e., length or width) suffices for mature specimens of a single species or family, but for larger studies, or when including immature specimens, at least the prosoma area (within the outline shape) should be used as a size estimator.

Insights into the Karyotype Evolution of Charinidae, the Early-Diverging Clade of Whip Spiders (Arachnida: Amblypygi)

Whip spiders (Amblypygi) represent an ancient order of tetrapulmonate arachnids with a low diversity. Their cytogenetic data are confined to only a few reports. Here, we analyzed the family Charinidae, a lineage almost at the base of the amblypygids, providing an insight into the ancestral traits and basic trajectories of amblypygid karyotype evolution. We performed Giemsa staining, selected banding techniques, and detected 18S ribosomal DNA and telomeric repeats by fluorescence in situ hybridization in four Charinus and five Sarax species. Both genera exhibit a wide range of diploid chromosome numbers (2n = 42-76 and 22-74 for Charinus and Sarax, respectively). The 2n reduction was accompanied by an increase of proportion of biarmed elements. We further revealed a single NOR site (probably an ancestral condition for charinids), the presence of a (TTAGG)n telomeric motif localized mostly at the chromosome ends, and an absence of heteromorphic sex chromosomes. Our data collectively suggest a high pace of karyotype repatterning in amblypygids, with probably a high ancestral 2n and its subsequent gradual reduction by fusions, and the action of pericentric inversions, similarly to what has been proposed for neoamblypygids. The possible contribution of fissions to charinid karyotype repatterning, however, cannot be fully ruled out.

Volcanism and palaeoclimate change drive diversification of the world's largest whip spider (Amblypygi)

The tropics contain many of the most biodiverse regions on Earth but the processes responsible for generating this diversity remain poorly understood. This study investigated the drivers of diversification in arthropods with stenotopic ecological requirements and limited dispersal capability using as a model the monotypic whip spider (Amblypygi) genus Acanthophrynus, widespread in the tropical deciduous forests of Mexico. We hypothesized that for these organisms, the tropical deciduous forests serve as a conduit for dispersal, with their disappearance imposing barriers. Given that these forests are located in a region of complex geological history and that they fluctuated in extent during the Pliocene-Pleistocene glacial/interglacial cycles we combine molecular divergence dating, palaeoclimatic niche modelling and ancestral area reconstruction to test if and when habitat fragmentation promoted diversification in Acanthophrynus. Concomitant with the expected role of landscape change, we demonstrate that orogeny of the Trans-Mexican Volcanic Belt, in the Late Miocene or Early Pliocene (6.95-5.21 million years ago), drove the earliest divergence of Acanthophrynus by vicariance. Similarly, as expected, the later onset of glaciations strongly impacted diversification. Whereas a more stable climate in the southern part of the distribution enabled further diversification, a marked loss of suitable habitat during the glaciations only allowed dispersal and diversification in the north to occur later, resulting in a lower overall diversity in this region. Barriers and diversification patterns identified in Acanthophrynus are reflected in the phylogeography of codistributed vertebrates and arthropods, emphasizing the profound impact of Trans-Mexican Volcanic Belt orogeny and glacial/interglacial cycles as drivers of diversification in the Mexican Neotropics.