after c16 Problem Solving with Phylogenetic systematics

Problem solving with Phylogenetic Systematic

Phylogenies are useful for examining biological and evolutionary problems. The following is from the work of Townsend et al. (2011).

The tiger chameleon is endemic to the Seychelles in the Indian Ocean. One hypothesis suggests that this chameleon evolved there as a result of the breakup of Gondwana. Another posits that the tiger chameleon colonized the Seychelles as a result of waif dispersal, from Africa, India, or Madagascar.

In addition to the Seychelles

In addition to the Seychelles, chameleons are found throughout sub-Saharan Africa, on Madagascar, and in southern Asia (i.e. the Indian subcontinent).

By reconstructing a phylogeny for the major lineages of chameleons, and mapping their geographical distributions on to this tree, one should be able to deduce the origin of tiger chameleons. However, a geological context would be useful to investigate the non-dispersal idea as well

Hypothesis 1:

Hypothesis 1: suggests that chameleons were always widespread across much of Africa, southern Asia, Madgascar, and the Seychelles, and speciation is partly due to the ancestral range being fragmented. This is phenomenon is vicariance.

A corollary of hypothesis 1 is that the clade of chameleons is relatively old, and originated before the breakup of Gondwana. For hypothesis 1, the ancestral chameleon is envisioned as widespread across much of Gondwana, and as the super continent fragmented, this resulted in speciation among chameleons.

Hypothesis 2:

Hypothesis 2: the origin of the tiger chameleon is the result of dispersal from Africa, India, or Madagascar, and so the origin time would not be tied to continental breakup.

Townsend and colleagues (2011) reconstructed the phylogeny of these reptiles, and found that the tiger chameleon is sister to a clade of African chameleons (genus Rieppeleon).

Moreover, molecular clock estimates suggest that the tiger chameleon originated 38.4 Ma.

An origin 38.4 Ma conflicts with the time..

An origin 38.4 Ma conflicts with the time (65 Ma) that geologists suggest that the Seychelles separated from a major Gondwanan land mass (viz. India).

The conflicting origin times and the observation that the tiger chameleon is nested with a clade of (mostly) African chameleons support the dispersal hypothesis.

The phylogeny informed by geographical and molecular cloc

The phylogeny informed by geographical and molecular clock data suggest strongly that Seychelle tiger chameleon probably originated in Africa.

At least one African chameleon (a pregnant female?) was carried there by chance, possibly on a tree that was uprooted and drifted in the Indian Ocean and swept past the Seychelles. The tree later beached on the Seychelles and the reptiles found a new home. Prior to Townsend et al.’s (2011) study, the tiger chameleon was classified as Calumma tigris. The authors resurrected the genus Archaius for the tiger chameleon (now Archaius tigris).

Vicariance (allopatric speciation) in montane birds

Vicariance (allopatric speciation mode 1), peripheral isolates (allopatric speciation mode 2), sympatric, and peripatric are the classic speciation modes.

Because of their ability to disperse widely as flying vertebrates, birds were generally thought to be candidates for sympatric speciation, which posits that speciation occurs among sympatrically distributed organisms, i.e. organisms with broadly overlapping ranges. However, phylogenetic biogeographic studies find that birds have speciated mainly vicariantly.

More on vicariance

In vicariance, populations of organisms are broken up because their habitat is fragmented; genetic differences accrue in the fragmented populations, and these eventually become distinct species.

Voelker et al. (2015) examined speciation is Old World montane birds called redstarts of the genus Phoenicurus. Voelker (2009) had previously studied speciation in Phoenicurus across Eurasia under the hypothesis that the genus had speciated in the past 6 million years as the result of glaciation promoting increasing aridity of central Asia during glacial maxima.

Voelker

Voelker (2009) did not have samples for several species of Phoenicurus, including one species endemic to northwestern Africa. Voelker et al. (2015) expanded the genetic sampling of this genus.

Voelker et al.’s (2015) phylogenetic results are presented with geographic range data and molecular clock estimates of divergence times. The authors concluded that most of the speciation in Phoenicurus has been vicariance (corroborating Voelker, 2009).

More on Voelker et al.

Voelker et al. (2015) analysis strongly suggested that the genus originated in the Himalayas.

Most Phoenicurus species live in montane habitats and this predisposes them to separation/fragmentation as high altitude habitats can act like islands but in this case can be separated by “seas” of lowlands. Voelker et al. (2015) found that sister species were distributed in separate mountain chains or, if distributed in the same mountain chains, occupied different mountains in the same range

In the Voelker et al. (2015) tree the geographic distributions are abbreviated W

In the Voelker et al. (2015) tree the geographic distributions are abbreviated W, C, E, H, etc. and broad ranges as HE, HCW, etc. The ranges on the terminal branches are used to determine the ancestral state at the common node, e.g. HC + H leads to decisive assignment of H to the common node (H “over” H). C “over” H is equivocal (i.e. state assignment is C or H).

State assignments for ranges at nodes are compared to states of sister taxa (nodes or terminal branches) downwards from tips of tree to the ingroup node (CH or H)

Mapping the distributions of the species on the Voelker et al.

Mapping the distributions of the species on the Voelker et al. (2015) tree and reconstructing states for nodes reveals that the ancestral Phoenicurus lived 7 to 6 million years ago in the Himalayas or the Himalayas + central Asia, and by 6 million years ago had speciated and given rise to the Ph. erythronotus and Ph. phoenicurus species groups.

Phoenicurus bicolor of the Phillippines is the sister species of Ph. fuliginosus (HE). The former species probably originated via peripheral isolates speciation, following dispersal of individuals of the latter species from East Asia just under 1 million years ago.

Drovetski et al. (2013)1 discovered similar patterns in their molecular….

Drovetski et al. (2013)1 discovered similar patterns in their molecular, phylogenetic, and biogeographic examination of Eurasian accentors (prunellids), songbirds of the genera Prunella and Laiscopus, most of which are montane.

For the historical biogeographical analysis, each prunellid species was coded as being present or absent in any of four areas: Western, Central and Eastern Palearctic, and the Himalayan region.

The biogeographic analysis revealed that prunellids …

The biogeographic analysis revealed that prunellids originated in the Himalayas about 14.8 million years ago (Drovetski et al., 2013). The two main subclades (the genera Prunella and Laiscopus) diverged about 7.31 million years ago.

2.1 to 1.7 million years ago (early Pleistocene) small accentors in the genus Prunella radiated, producing four divergence events and dispersed out of the Himalyas and westward across Eurasia. Three of divergences resulted in allopatrically separated species. The fourth involved range overlap between sister species.

Prunella koslowi and Prunella fulvescens are sister taxa that overlap ranges in the Himalayas. However, these two species occupy different habitats in their respective ranges: P. koslowi lives in thin scrub, semi desert habitat and P. fulvescens prefers shrubs near the timberline in the mountains (plesiomorphic habitat preference for accentors).

Vicariance in shrimp

South America was isolated from other land mass for over 100 million years. The Isthmus of Panama formed 3.5 to 3 million years ago, joining South America and North America.

The formation of the Panama land bridge famously allowed land mammals, etc. of North America to disperse into South America, and vice versa. Opossums, armadillos, and sloths migrated north into southern North America, and camelids, horses, rabbits, and foxes dispersed south into South America.

The formation of the Panama land bridge also affected marine animals.

The formation of the Panama land bridge also affected marine animals. Prior to its formation, what is now the Caribbean Sea and the eastern Pacific Ocean were connected (via the "Caribbean Seaway") and many marine animals ranged through this transitional area between the Atlantic and Pacific oceans. Knowlton et al. (1993) investigated the impact of the Isthmus of Panama on the evolutionary history of the shrimp genus Alpheus. They reconstructed the interrelationships of 14 species of the genus and discovered 7 Caribbean-Pacific species pairs.

The sister-group pairings of Caribbean and Pacific shrimp

The sister-group pairings of Caribbean and Pacific shrimp indicate that the formation of the isthmus fragmented formerly widespread (ancestral) species into geographically separated sister species.

Knowlton et al.'s (1993) results also indicate that 7 speciation events were triggered by the formation of the isthmus, they were not simultaneous. The staggered speciation events are the result of ancestral shrimp occupying different depths, such that deep-dwelling populations were fragmented first, followed by shallower populations, as the isthmus formed

Speciation in Hawaiian swordtail crickets

Laupala is a genus of swordtail crickets known only from the Hawaiian islands.

The Hawaiian islands are the youngest part of a chain of 125 volcanoes stretching thousands of kilometres across the Pacific Ocean. Kauai is the oldest of the main islands at 5.1 million years of age (Ma), Oahu is 5 Ma, and the big island of Hawaii is 460,000 years old. The northwestern-most island, Kure Atoll, is the oldest at roughly 28 Ma.

Observation and Hypothesis options

Observation: the swordtail crickets on Maui exhibit the greatest morphological and acoustic differences among all the species.

Hypothesis 1: Laupala originated on Maui and then colonized the other islands.

Hypothesis 2: Laupala is "tracking" the islands, so the phylogenetically older (most basal) species should be found on the older islands, and the phylogenetically youngest (most recent) species should be found on the geologically youngest island

Ritchie and Macías Garcia’s

Ritchie and Macías Garcia’s (2005) cladogram suggests that the species are tracking the islands (H2): the phylogenetically oldest species are found on the oldest islands Kauai and Oahu, and the phylogenetically younger species are found on Maui and Hawaii.

The morphological and acoustic diversity attributed to swordtail crickets on Maui is the result of two separate colonizations of the island from Oahu and time (Molokai and Maui are 1.2 Ma). The seven species on the big island of Hawaii are the youngest: they must have originated in the past 400,000 years

How Hawaii was formed

Kauai→ Oahu→ Molokai/Maui → Hawaii

Swordtail crickets experienced

Swordtail crickets experienced at least 5 dispersal events over the past 5 million years. Crickets from old(er) islands colonized younger islands, as the islands appeared. This was probably a result of waif dispersal as Laupala crickets are flightless